Slicer Wiki - User contributions [en]

Documentation/4.1/SlicerApplication/LookupTables/TractographyColors

2012-08-07T15:03:14Z

Demian:

{{documentation/{{documentation/version}}/TractographyColors}}


*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].

This is the look-up table for the parcellation of the white matter of the brain.
*Authors: Ron Kikinis, Demian Wassermann, Marianna Jakab

==Lookup table==

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|background
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|
|-
|1
|CC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Corpus Callosum
|-
|2
|CC genu
|style="background:rgb(241,214,145)"|rgb(241,214,145)
|Genu of the Corpus Callosum
|-
|3
|CC body
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|Body of the Corpus Callosum
|-
|4
|CC splenium
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|Splenium of the Corpus Callosum
|-
|5
|r AC
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right arcuate fasciculus
|-
|6
|l AC
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|left arcuate fasciculus
|-
|7
|r IOFF
|style="background:rgb(144,238,144)"|rgb(144,238,144)
|right inferior occipito-frontal fasciculus
|-
|8
|l IOFF
|style="background:rgb(192,104,88)"|rgb(192,104,88)
|left inferior occipito-frontal fasciculus
|-
|9
|r ILF
|style="background:rgb(220,245,20)"|rgb(220,245,20)
|right inferior longitudinal fasciculus
|-
|10
|l ILF
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left inferior longitudinal fasciculus
|-
|11
|r UNC
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|right uncinate fasciculus
|-
|12
|l UNC
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|left uncinate fasciculus
|-
|13
|r CST
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|right cortico-spinal tract
|-
|14
|l CST
|style="background:rgb(250,250,210)"|rgb(250,250,210)
|left cortico-spinal tract
|-
|15
|r OR
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right optic radiation
|-
|16
|l OR
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|left optic radiation
|-
|17
|r CB
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right cingulate bundle
|-
|18
|l CB
|style="background:rgb(183,156,220)"|rgb(183,156,220)
|left cingulate bundle
|-
|19
|r SLF 1
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|right superior longitudinal fasciculus 1
|-
|20
|l SLF 1
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|left superior longitudinal fasciculus 1
|-
|21
|r SLF 2
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|right superior longitudinal fasciculus 2
|-
|22
|l SLF 2
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|left superior longitudinal fasciculus 2
|-
|23
|r SLF 3
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|right superior longitudinal fasciculus 3
|-
|24
|l SLF 3
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|left superior longitudinal fasciculus 3
|-
|25
|r MDLF
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|right middle longitudinal fasciculus
|-
|26
|l MDLF
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|left middle longitudinal fasciculus
|-
|27
|r EC
|style="background:rgb(214,230,130)"|rgb(214,230,130)
|right extreme capsule
|-
|28
|l EC
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left extreme capsule
|-
|29
|DHC
|style="background:rgb(218,255,255)"|rgb(218,255,255)
|Dorsal hippocampal comissure
|-
|30
|AnC
|style="background:rgb(170,250,250)"|rgb(170,250,250)
|Anterior Comissure
|-
|31
|FC
|style="background:rgb(140,224,228)"|rgb(140,224,228)
|Forniceal Comissure
|-
|32
|r SOFF
|style="background:rgb(188,65,28)"|rgb(188,65,28)
|right superior occipito-frontal fasciculus
|-
|33
|l SOFF
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|left superior occipito-frontal fasciculus
|-
|34
|l CT
|style="background:rgb(145,60,66)"|rgb(145,60,66)
|left cortico-thalamical pathways
|-
|35
|r CT
|style="background:rgb(150,98,83)"|rgb(150,98,83)
|right cortico-thalamical pathways
|-
|36
|l CS
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|left cortico-striatal pathways
|-
|37
|r CS
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right cortico-striatal pathways
|-
|38
|l CP
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|left cortico-pontine projections
|-
|39
|r CP
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|right cortico-pontine projections
|-
|40
|PT
|style="background:rgb(68,131,98)"|rgb(68,131,98)
|Pontine Tract
|-
|41
|PC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Posterior comissure
|-
|42
|U
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|short cortico-cortical pathway
|-
|43
|left frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|44
|right temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|45
|left temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|46
|right parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|47
|left parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|48
|right occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|49
|left occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|50
|right insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|51
|left insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|52
|right limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|53
|left limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|54
|right striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|55
|left striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|56
|right caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|57
|left caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|58
|right putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|59
|left putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|60
|right pullidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|61
|left pallidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|62
|right amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|63
|left amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|64
|diencephalon
|style="background:rgb(69,110,53)"|rgb(69,110,53)
|
|-
|65
|thalamus
|style="background:rgb(166,113,137)"|rgb(166,113,137)
|
|-
|66
|right thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|67
|left thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|68
|pineal gland
|style="background:rgb(253,135,192)"|rgb(253,135,192)
|
|-
|69
|midbrain
|style="background:rgb(145,92,109)"|rgb(145,92,109)
|
|-
|70
|substantia nigra
|style="background:rgb(46,101,131)"|rgb(46,101,131)
|
|-
|71
|right substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|72
|left substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|73
|cerebral white matter
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|74
|right superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|75
|left superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|76
|right inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|77
|left inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|78
|right arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|79
|left arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|80
|right uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|81
|left uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|82
|right cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|83
|left cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|84
|projection fibers
|style="background:rgb(126,126,55)"|rgb(126,126,55)
|
|-
|85
|right corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|86
|left corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|87
|right optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|88
|left optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|89
|right medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|90
|left medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|91
|right superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|92
|left superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|93
|right middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|94
|left middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|95
|right inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|96
|left inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|97
|optic chiasm
|style="background:rgb(99,106,24)"|rgb(99,106,24)
|
|-
|98
|right optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|99
|left optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|100
|right fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|101
|left fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|102
|commissural fibers
|style="background:rgb(138,95,74)"|rgb(138,95,74)
|
|-
|103
|corpus callosum
|style="background:rgb(97,113,158)"|rgb(97,113,158)
|
|-
|104
|posterior commissure
|style="background:rgb(126,161,197)"|rgb(126,161,197)
|
|-
|105
|cerebellar white matter
|style="background:rgb(194,195,164)"|rgb(194,195,164)
|
|-
|106
|CSF space
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|107
|ventricles of brain
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|108
|right lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|109
|left lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|110
|right third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|111
|left third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|112
|cerebral aqueduct
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|113
|fourth ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|114
|subarachnoid space
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|115
|spinal cord
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|116
|gray matter of spinal cord
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|117
|white matter of spinal cord
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|118
|endocrine system of brain
|style="background:rgb(82,174,128)"|rgb(82,174,128)
|
|-
|119
|pituitary gland
|style="background:rgb(57,157,110)"|rgb(57,157,110)
|
|-
|120
|adenohypophysis
|style="background:rgb(60,143,83)"|rgb(60,143,83)
|
|-
|121
|neurohypophysis
|style="background:rgb(92,162,109)"|rgb(92,162,109)
|
|-
|122
|meninges
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|123
|dura mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|124
|arachnoid
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|125
|pia mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|126
|muscles of head
|style="background:rgb(201,121,77)"|rgb(201,121,77)
|
|-
|127
|salivary glands
|style="background:rgb(70,163,117)"|rgb(70,163,117)
|
|-
|128
|lips
|style="background:rgb(188,91,95)"|rgb(188,91,95)
|
|-
|129
|nose
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|130
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|131
|soft palate
|style="background:rgb(182,105,107)"|rgb(182,105,107)
|
|-
|132
|right inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|133
|left inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|134
|right external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|135
|left external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|136
|right middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|137
|left middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|138
|right eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|139
|left eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|140
|skull
|style="background:rgb(241,213,144)"|rgb(241,213,144)
|
|-
|141
|right frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|142
|left frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|143
|right parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|144
|left parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|145
|right temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|146
|left temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|147
|right sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|148
|left sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|149
|right ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|150
|left ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|151
|occipital bone
|style="background:rgb(255,230,138)"|rgb(255,230,138)
|
|-
|152
|maxilla
|style="background:rgb(196,172,68)"|rgb(196,172,68)
|
|-
|153
|right zygomatic bone
|style="background:rgb(255,255,167)"|rgb(255,255,167)
|
|-
|154
|right lacrimal bone
|style="background:rgb(255,250,160)"|rgb(255,250,160)
|
|-
|155
|vomer bone
|style="background:rgb(255,237,145)"|rgb(255,237,145)
|
|-
|156
|right palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|157
|left palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|158
|mandible
|style="background:rgb(222,198,101)"|rgb(222,198,101)
|
|-
|159
|neck
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|160
|muscles of neck
|style="background:rgb(213,124,109)"|rgb(213,124,109)
|
|-
|161
|pharynx
|style="background:rgb(184,105,108)"|rgb(184,105,108)
|
|-
|162
|larynx
|style="background:rgb(150,208,243)"|rgb(150,208,243)
|
|-
|163
|thyroid gland
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|164
|right parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|165
|left parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|166
|skeleton of neck
|style="background:rgb(242,206,142)"|rgb(242,206,142)
|
|-
|167
|hyoid bone
|style="background:rgb(250,210,139)"|rgb(250,210,139)
|
|-
|168
|cervical vertebral column
|style="background:rgb(255,255,207)"|rgb(255,255,207)
|
|-
|169
|thorax
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|170
|trachea
|style="background:rgb(182,228,255)"|rgb(182,228,255)
|
|-
|171
|bronchi
|style="background:rgb(175,216,244)"|rgb(175,216,244)
|
|-
|172
|right lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|173
|left lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|174
|superior lobe of right lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|175
|superior lobe of left lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|176
|middle lobe of right lung
|style="background:rgb(202,164,140)"|rgb(202,164,140)
|
|-
|177
|inferior lobe of right lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|178
|inferior lobe of left lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|179
|pleura
|style="background:rgb(255,245,217)"|rgb(255,245,217)
|
|-
|180
|heart
|style="background:rgb(206,110,84)"|rgb(206,110,84)
|
|-
|181
|right atrium
|style="background:rgb(210,115,89)"|rgb(210,115,89)
|
|-
|182
|left atrium
|style="background:rgb(203,108,81)"|rgb(203,108,81)
|
|-
|183
|atrial septum
|style="background:rgb(233,138,112)"|rgb(233,138,112)
|
|-
|184
|ventricular septum
|style="background:rgb(195,100,73)"|rgb(195,100,73)
|
|-
|185
|right ventricle of heart
|style="background:rgb(181,85,57)"|rgb(181,85,57)
|
|-
|186
|left ventricle of heart
|style="background:rgb(152,55,13)"|rgb(152,55,13)
|
|-
|187
|mitral valve
|style="background:rgb(159,63,27)"|rgb(159,63,27)
|
|-
|188
|tricuspid valve
|style="background:rgb(166,70,38)"|rgb(166,70,38)
|
|-
|189
|aortic valve
|style="background:rgb(218,123,97)"|rgb(218,123,97)
|
|-
|190
|pulmonary valve
|style="background:rgb(225,130,104)"|rgb(225,130,104)
|
|-
|191
|aorta
|style="background:rgb(224,97,76)"|rgb(224,97,76)
|
|-
|192
|pericardium
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|193
|pericardial cavity
|style="background:rgb(184,122,154)"|rgb(184,122,154)
|
|-
|194
|esophagus
|style="background:rgb(211,171,143)"|rgb(211,171,143)
|
|-
|195
|thymus
|style="background:rgb(47,150,103)"|rgb(47,150,103)
|
|-
|196
|mediastinum
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|197
|skin of thoracic wall
|style="background:rgb(173,121,88)"|rgb(173,121,88)
|
|-
|198
|muscles of thoracic wall
|style="background:rgb(188,95,76)"|rgb(188,95,76)
|
|-
|199
|skeleton of thorax
|style="background:rgb(255,239,172)"|rgb(255,239,172)
|
|-
|200
|thoracic vertebral column
|style="background:rgb(226,202,134)"|rgb(226,202,134)
|
|-
|201
|ribs
|style="background:rgb(253,232,158)"|rgb(253,232,158)
|
|-
|202
|sternum
|style="background:rgb(244,217,154)"|rgb(244,217,154)
|
|-
|203
|right clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|204
|left clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|205
|abdominal cavity
|style="background:rgb(186,124,161)"|rgb(186,124,161)
|
|-
|206
|abdomen
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|207
|peritoneum
|style="background:rgb(255,255,220)"|rgb(255,255,220)
|
|-
|208
|omentum
|style="background:rgb(234,234,194)"|rgb(234,234,194)
|
|-
|209
|peritoneal cavity
|style="background:rgb(204,142,178)"|rgb(204,142,178)
|
|-
|210
|retroperitoneal space
|style="background:rgb(180,119,153)"|rgb(180,119,153)
|
|-
|211
|stomach
|style="background:rgb(216,132,105)"|rgb(216,132,105)
|
|-
|212
|duodenum
|style="background:rgb(255,253,229)"|rgb(255,253,229)
|
|-
|213
|small bowel
|style="background:rgb(205,167,142)"|rgb(205,167,142)
|
|-
|214
|colon
|style="background:rgb(204,168,143)"|rgb(204,168,143)
|
|-
|215
|anus
|style="background:rgb(255,224,199)"|rgb(255,224,199)
|
|-
|216
|liver
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|217
|biliary tree
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|218
|gallbladder
|style="background:rgb(139,150,98)"|rgb(139,150,98)
|
|-
|219
|pancreas
|style="background:rgb(249,180,111)"|rgb(249,180,111)
|
|-
|220
|spleen
|style="background:rgb(157,108,162)"|rgb(157,108,162)
|
|-
|221
|urinary system
|style="background:rgb(203,136,116)"|rgb(203,136,116)
|
|-
|222
|right kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|223
|left kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|224
|right ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|225
|left ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|226
|urinary bladder
|style="background:rgb(222,154,132)"|rgb(222,154,132)
|
|-
|227
|urethra
|style="background:rgb(124,186,223)"|rgb(124,186,223)
|
|-
|228
|right adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|229
|left adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|230
|female internal genitalia
|style="background:rgb(244,170,147)"|rgb(244,170,147)
|
|-
|231
|uterus
|style="background:rgb(255,181,158)"|rgb(255,181,158)
|
|-
|232
|right fallopian tube
|style="background:rgb(255,190,165)"|rgb(255,190,165)
|
|-
|233
|left fallopian tube
|style="background:rgb(227,153,130)"|rgb(227,153,130)
|
|-
|234
|right ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|235
|left ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|236
|vagina
|style="background:rgb(193,123,103)"|rgb(193,123,103)
|
|-
|237
|male internal genitalia
|style="background:rgb(216,146,127)"|rgb(216,146,127)
|
|-
|238
|prostate
|style="background:rgb(230,158,140)"|rgb(230,158,140)
|
|-
|239
|right seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|240
|left seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|241
|right deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|242
|left deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|243
|skin of abdominal wall
|style="background:rgb(177,124,92)"|rgb(177,124,92)
|
|-
|244
|muscles of abdominal wall
|style="background:rgb(171,85,68)"|rgb(171,85,68)
|
|-
|245
|skeleton of abdomen
|style="background:rgb(217,198,131)"|rgb(217,198,131)
|
|-
|246
|lumbar vertebral column
|style="background:rgb(212,188,102)"|rgb(212,188,102)
|
|-
|247
|female external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|248
|male external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|249
|skeleton of upper limb
|style="background:rgb(198,175,125)"|rgb(198,175,125)
|
|-
|250
|muscles of upper limb
|style="background:rgb(194,98,79)"|rgb(194,98,79)
|
|-
|251
|right upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|252
|left upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|253
|right shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|254
|left shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|255
|right arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|256
|left arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|257
|right elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|258
|left elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|259
|right forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|260
|left forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|261
|right wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|262
|left wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|263
|right hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|264
|left hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|265
|skeleton of lower limb
|style="background:rgb(255,238,170)"|rgb(255,238,170)
|
|-
|266
|muscles of lower limb
|style="background:rgb(206,111,93)"|rgb(206,111,93)
|
|-
|267
|right lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|268
|left lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|269
|right hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|270
|left hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|271
|right thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|272
|left thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|273
|right knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|274
|left knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|275
|right leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|276
|left leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|277
|right foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|278
|left foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|279
|peripheral nervous system
|style="background:rgb(216,186,0)"|rgb(216,186,0)
|
|-
|280
|autonomic nerve
|style="background:rgb(255,226,77)"|rgb(255,226,77)
|
|-
|281
|sympathetic trunk
|style="background:rgb(255,243,106)"|rgb(255,243,106)
|
|-
|282
|cranial nerves
|style="background:rgb(255,234,92)"|rgb(255,234,92)
|
|-
|283
|vagus nerve
|style="background:rgb(240,210,35)"|rgb(240,210,35)
|
|-
|284
|peripheral nerve
|style="background:rgb(224,194,0)"|rgb(224,194,0)
|
|-
|285
|circulatory system
|style="background:rgb(213,99,79)"|rgb(213,99,79)
|
|-
|286
|systemic arterial system
|style="background:rgb(217,102,81)"|rgb(217,102,81)
|
|-
|287
|systemic venous system
|style="background:rgb(0,147,202)"|rgb(0,147,202)
|
|-
|288
|pulmonary arterial system
|style="background:rgb(0,122,171)"|rgb(0,122,171)
|
|-
|289
|pulmonary venous system
|style="background:rgb(186,77,64)"|rgb(186,77,64)
|
|-
|290
|lymphatic system
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|291
|needle
|style="background:rgb(240,255,30)"|rgb(240,255,30)
|
|-
|292
|region 0
|style="background:rgb(185,232,61)"|rgb(185,232,61)
|
|-
|293
|region 1
|style="background:rgb(0,226,255)"|rgb(0,226,255)
|
|-
|294
|region 2
|style="background:rgb(251,159,255)"|rgb(251,159,255)
|
|-
|295
|region 3
|style="background:rgb(230,169,29)"|rgb(230,169,29)
|
|-
|296
|region 4
|style="background:rgb(0,194,113)"|rgb(0,194,113)
|
|-
|297
|region 5
|style="background:rgb(104,160,249)"|rgb(104,160,249)
|
|-
|298
|region 6
|style="background:rgb(221,108,158)"|rgb(221,108,158)
|
|-
|299
|region 7
|style="background:rgb(137,142,0)"|rgb(137,142,0)
|
|-
|300
|region 8
|style="background:rgb(230,70,0)"|rgb(230,70,0)
|
|-
|301
|region 9
|style="background:rgb(0,147,0)"|rgb(0,147,0)
|
|-
|302
|region 10
|style="background:rgb(0,147,248)"|rgb(0,147,248)
|
|-
|303
|region 11
|style="background:rgb(231,0,206)"|rgb(231,0,206)
|
|-
|304
|region 12
|style="background:rgb(129,78,0)"|rgb(129,78,0)
|
|-
|305
|region 13
|style="background:rgb(0,116,0)"|rgb(0,116,0)
|
|-
|306
|region 14
|style="background:rgb(0,0,255)"|rgb(0,0,255)
|
|-
|307
|region 15
|style="background:rgb(157,0,0)"|rgb(157,0,0)
|
|-
|308
|unknown
|style="background:rgb(100,100,130)"|rgb(100,100,130)
|
|-
|309
|cyst
|style="background:rgb(205,205,100)"|rgb(205,205,100)
|
|-
|}

Documentation/4.1/SlicerApplication/LookupTables/TractographyColors

2012-08-07T14:23:46Z

Demian:

{{documentation/{{documentation/version}}/TractographyColors}}


*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].

This is the look-up table for the parcellation of the white matter of the brain.
*Authors: Ron Kikinis, Demian Wassermann, Marianna Jakab

==Lookup table==

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|background
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|
|-
|1
|CC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Corpus Callosum
|-
|2
|CC genu
|style="background:rgb(241,214,145)"|rgb(241,214,145)
|Genu of the Corpus Callosum
|-
|3
|CC body
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|Body of the Corpus Callosum
|-
|4
|CC splenium
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|Splenium of the Corpus Callosum
|-
|5
|r AC
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right arcuate fasciculus
|-
|6
|l AC
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|left arcuate fasciculus
|-
|7
|r IOFF
|style="background:rgb(144,238,144)"|rgb(144,238,144)
|right inferior occipito-frontal fasciculus
|-
|8
|l IOFF
|style="background:rgb(192,104,88)"|rgb(192,104,88)
|left inferior occipito-frontal fasciculus
|-
|9
|r ILF
|style="background:rgb(220,245,20)"|rgb(220,245,20)
|right inferior longitudinal fasciculus
|-
|10
|l ILF
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left inferior longitudinal fasciculus
|-
|11
|r UNC
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|right uncinate fasciculus
|-
|12
|l UNC
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|left uncinate fasciculus
|-
|13
|r CST
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|right cortico-spinal tract
|-
|14
|l CST
|style="background:rgb(250,250,210)"|rgb(250,250,210)
|left cortico-spinal tract
|-
|15
|r OR
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right optic radiation
|-
|16
|l OR
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|left optic radiation
|-
|17
|r CB
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right cingulate bundle
|-
|18
|l CB
|style="background:rgb(183,156,220)"|rgb(183,156,220)
|left cingulate bundle
|-
|19
|r SLF 1
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|right superior longitudinal fasciculus 1
|-
|20
|l SLF 1
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|left superior longitudinal fasciculus 1
|-
|21
|r SLF 2
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|right superior longitudinal fasciculus 2
|-
|22
|l SLF 2
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|left superior longitudinal fasciculus 2
|-
|23
|r SLF 3
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|right superior longitudinal fasciculus 3
|-
|24
|l SLF 3
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|left superior longitudinal fasciculus 3
|-
|25
|r MDLF
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|right middle longitudinal fasciculus
|-
|26
|l MDLF
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|left middle longitudinal fasciculus
|-
|27
|r EC
|style="background:rgb(214,230,130)"|rgb(214,230,130)
|right extreme capsule
|-
|28
|l EC
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left extreme capsule
|-
|29
|DHC
|style="background:rgb(218,255,255)"|rgb(218,255,255)
|Dorsal hippocampal comissure
|-
|30
|AnC
|style="background:rgb(170,250,250)"|rgb(170,250,250)
|Anterior Comissure
|-
|31
|FC
|style="background:rgb(140,224,228)"|rgb(140,224,228)
|Forniceal Comissure
|-
|32
|r SOFF
|style="background:rgb(188,65,28)"|rgb(188,65,28)
|right superior occipito-frontal fasciculus
|-
|33
|l SOFF
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|left superior occipito-frontal fasciculus
|-
|34
|l CT
|style="background:rgb(145,60,66)"|rgb(145,60,66)
|left cortico-thalamical pathways
|-
|35
|r CT
|style="background:rgb(150,98,83)"|rgb(150,98,83)
|right cortico-thalamical pathways
|-
|36
|l SC
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|left cortico-striatal pathways
|-
|37
|r SC
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right cortico-striatal pathways
|-
|38
|l CP
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|left cortico-pontine projections
|-
|39
|r CP
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|right cortico-pontine projections
|-
|40
|PT
|style="background:rgb(68,131,98)"|rgb(68,131,98)
|Pontine Tract
|-
|41
|PC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Posterior comissure
|-
|42
|U
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|short cortico-cortical pathway
|-
|43
|left frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|44
|right temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|45
|left temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|46
|right parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|47
|left parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|48
|right occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|49
|left occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|50
|right insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|51
|left insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|52
|right limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|53
|left limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|54
|right striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|55
|left striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|56
|right caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|57
|left caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|58
|right putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|59
|left putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|60
|right pullidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|61
|left pallidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|62
|right amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|63
|left amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|64
|diencephalon
|style="background:rgb(69,110,53)"|rgb(69,110,53)
|
|-
|65
|thalamus
|style="background:rgb(166,113,137)"|rgb(166,113,137)
|
|-
|66
|right thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|67
|left thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|68
|pineal gland
|style="background:rgb(253,135,192)"|rgb(253,135,192)
|
|-
|69
|midbrain
|style="background:rgb(145,92,109)"|rgb(145,92,109)
|
|-
|70
|substantia nigra
|style="background:rgb(46,101,131)"|rgb(46,101,131)
|
|-
|71
|right substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|72
|left substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|73
|cerebral white matter
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|74
|right superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|75
|left superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|76
|right inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|77
|left inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|78
|right arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|79
|left arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|80
|right uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|81
|left uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|82
|right cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|83
|left cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|84
|projection fibers
|style="background:rgb(126,126,55)"|rgb(126,126,55)
|
|-
|85
|right corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|86
|left corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|87
|right optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|88
|left optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|89
|right medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|90
|left medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|91
|right superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|92
|left superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|93
|right middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|94
|left middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|95
|right inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|96
|left inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|97
|optic chiasm
|style="background:rgb(99,106,24)"|rgb(99,106,24)
|
|-
|98
|right optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|99
|left optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|100
|right fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|101
|left fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|102
|commissural fibers
|style="background:rgb(138,95,74)"|rgb(138,95,74)
|
|-
|103
|corpus callosum
|style="background:rgb(97,113,158)"|rgb(97,113,158)
|
|-
|104
|posterior commissure
|style="background:rgb(126,161,197)"|rgb(126,161,197)
|
|-
|105
|cerebellar white matter
|style="background:rgb(194,195,164)"|rgb(194,195,164)
|
|-
|106
|CSF space
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|107
|ventricles of brain
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|108
|right lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|109
|left lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|110
|right third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|111
|left third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|112
|cerebral aqueduct
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|113
|fourth ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|114
|subarachnoid space
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|115
|spinal cord
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|116
|gray matter of spinal cord
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|117
|white matter of spinal cord
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|118
|endocrine system of brain
|style="background:rgb(82,174,128)"|rgb(82,174,128)
|
|-
|119
|pituitary gland
|style="background:rgb(57,157,110)"|rgb(57,157,110)
|
|-
|120
|adenohypophysis
|style="background:rgb(60,143,83)"|rgb(60,143,83)
|
|-
|121
|neurohypophysis
|style="background:rgb(92,162,109)"|rgb(92,162,109)
|
|-
|122
|meninges
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|123
|dura mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|124
|arachnoid
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|125
|pia mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|126
|muscles of head
|style="background:rgb(201,121,77)"|rgb(201,121,77)
|
|-
|127
|salivary glands
|style="background:rgb(70,163,117)"|rgb(70,163,117)
|
|-
|128
|lips
|style="background:rgb(188,91,95)"|rgb(188,91,95)
|
|-
|129
|nose
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|130
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|131
|soft palate
|style="background:rgb(182,105,107)"|rgb(182,105,107)
|
|-
|132
|right inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|133
|left inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|134
|right external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|135
|left external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|136
|right middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|137
|left middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|138
|right eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|139
|left eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|140
|skull
|style="background:rgb(241,213,144)"|rgb(241,213,144)
|
|-
|141
|right frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|142
|left frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|143
|right parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|144
|left parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|145
|right temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|146
|left temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|147
|right sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|148
|left sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|149
|right ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|150
|left ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|151
|occipital bone
|style="background:rgb(255,230,138)"|rgb(255,230,138)
|
|-
|152
|maxilla
|style="background:rgb(196,172,68)"|rgb(196,172,68)
|
|-
|153
|right zygomatic bone
|style="background:rgb(255,255,167)"|rgb(255,255,167)
|
|-
|154
|right lacrimal bone
|style="background:rgb(255,250,160)"|rgb(255,250,160)
|
|-
|155
|vomer bone
|style="background:rgb(255,237,145)"|rgb(255,237,145)
|
|-
|156
|right palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|157
|left palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|158
|mandible
|style="background:rgb(222,198,101)"|rgb(222,198,101)
|
|-
|159
|neck
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|160
|muscles of neck
|style="background:rgb(213,124,109)"|rgb(213,124,109)
|
|-
|161
|pharynx
|style="background:rgb(184,105,108)"|rgb(184,105,108)
|
|-
|162
|larynx
|style="background:rgb(150,208,243)"|rgb(150,208,243)
|
|-
|163
|thyroid gland
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|164
|right parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|165
|left parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|166
|skeleton of neck
|style="background:rgb(242,206,142)"|rgb(242,206,142)
|
|-
|167
|hyoid bone
|style="background:rgb(250,210,139)"|rgb(250,210,139)
|
|-
|168
|cervical vertebral column
|style="background:rgb(255,255,207)"|rgb(255,255,207)
|
|-
|169
|thorax
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|170
|trachea
|style="background:rgb(182,228,255)"|rgb(182,228,255)
|
|-
|171
|bronchi
|style="background:rgb(175,216,244)"|rgb(175,216,244)
|
|-
|172
|right lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|173
|left lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|174
|superior lobe of right lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|175
|superior lobe of left lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|176
|middle lobe of right lung
|style="background:rgb(202,164,140)"|rgb(202,164,140)
|
|-
|177
|inferior lobe of right lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|178
|inferior lobe of left lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|179
|pleura
|style="background:rgb(255,245,217)"|rgb(255,245,217)
|
|-
|180
|heart
|style="background:rgb(206,110,84)"|rgb(206,110,84)
|
|-
|181
|right atrium
|style="background:rgb(210,115,89)"|rgb(210,115,89)
|
|-
|182
|left atrium
|style="background:rgb(203,108,81)"|rgb(203,108,81)
|
|-
|183
|atrial septum
|style="background:rgb(233,138,112)"|rgb(233,138,112)
|
|-
|184
|ventricular septum
|style="background:rgb(195,100,73)"|rgb(195,100,73)
|
|-
|185
|right ventricle of heart
|style="background:rgb(181,85,57)"|rgb(181,85,57)
|
|-
|186
|left ventricle of heart
|style="background:rgb(152,55,13)"|rgb(152,55,13)
|
|-
|187
|mitral valve
|style="background:rgb(159,63,27)"|rgb(159,63,27)
|
|-
|188
|tricuspid valve
|style="background:rgb(166,70,38)"|rgb(166,70,38)
|
|-
|189
|aortic valve
|style="background:rgb(218,123,97)"|rgb(218,123,97)
|
|-
|190
|pulmonary valve
|style="background:rgb(225,130,104)"|rgb(225,130,104)
|
|-
|191
|aorta
|style="background:rgb(224,97,76)"|rgb(224,97,76)
|
|-
|192
|pericardium
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|193
|pericardial cavity
|style="background:rgb(184,122,154)"|rgb(184,122,154)
|
|-
|194
|esophagus
|style="background:rgb(211,171,143)"|rgb(211,171,143)
|
|-
|195
|thymus
|style="background:rgb(47,150,103)"|rgb(47,150,103)
|
|-
|196
|mediastinum
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|197
|skin of thoracic wall
|style="background:rgb(173,121,88)"|rgb(173,121,88)
|
|-
|198
|muscles of thoracic wall
|style="background:rgb(188,95,76)"|rgb(188,95,76)
|
|-
|199
|skeleton of thorax
|style="background:rgb(255,239,172)"|rgb(255,239,172)
|
|-
|200
|thoracic vertebral column
|style="background:rgb(226,202,134)"|rgb(226,202,134)
|
|-
|201
|ribs
|style="background:rgb(253,232,158)"|rgb(253,232,158)
|
|-
|202
|sternum
|style="background:rgb(244,217,154)"|rgb(244,217,154)
|
|-
|203
|right clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|204
|left clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|205
|abdominal cavity
|style="background:rgb(186,124,161)"|rgb(186,124,161)
|
|-
|206
|abdomen
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|207
|peritoneum
|style="background:rgb(255,255,220)"|rgb(255,255,220)
|
|-
|208
|omentum
|style="background:rgb(234,234,194)"|rgb(234,234,194)
|
|-
|209
|peritoneal cavity
|style="background:rgb(204,142,178)"|rgb(204,142,178)
|
|-
|210
|retroperitoneal space
|style="background:rgb(180,119,153)"|rgb(180,119,153)
|
|-
|211
|stomach
|style="background:rgb(216,132,105)"|rgb(216,132,105)
|
|-
|212
|duodenum
|style="background:rgb(255,253,229)"|rgb(255,253,229)
|
|-
|213
|small bowel
|style="background:rgb(205,167,142)"|rgb(205,167,142)
|
|-
|214
|colon
|style="background:rgb(204,168,143)"|rgb(204,168,143)
|
|-
|215
|anus
|style="background:rgb(255,224,199)"|rgb(255,224,199)
|
|-
|216
|liver
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|217
|biliary tree
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|218
|gallbladder
|style="background:rgb(139,150,98)"|rgb(139,150,98)
|
|-
|219
|pancreas
|style="background:rgb(249,180,111)"|rgb(249,180,111)
|
|-
|220
|spleen
|style="background:rgb(157,108,162)"|rgb(157,108,162)
|
|-
|221
|urinary system
|style="background:rgb(203,136,116)"|rgb(203,136,116)
|
|-
|222
|right kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|223
|left kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|224
|right ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|225
|left ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|226
|urinary bladder
|style="background:rgb(222,154,132)"|rgb(222,154,132)
|
|-
|227
|urethra
|style="background:rgb(124,186,223)"|rgb(124,186,223)
|
|-
|228
|right adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|229
|left adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|230
|female internal genitalia
|style="background:rgb(244,170,147)"|rgb(244,170,147)
|
|-
|231
|uterus
|style="background:rgb(255,181,158)"|rgb(255,181,158)
|
|-
|232
|right fallopian tube
|style="background:rgb(255,190,165)"|rgb(255,190,165)
|
|-
|233
|left fallopian tube
|style="background:rgb(227,153,130)"|rgb(227,153,130)
|
|-
|234
|right ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|235
|left ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|236
|vagina
|style="background:rgb(193,123,103)"|rgb(193,123,103)
|
|-
|237
|male internal genitalia
|style="background:rgb(216,146,127)"|rgb(216,146,127)
|
|-
|238
|prostate
|style="background:rgb(230,158,140)"|rgb(230,158,140)
|
|-
|239
|right seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|240
|left seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|241
|right deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|242
|left deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|243
|skin of abdominal wall
|style="background:rgb(177,124,92)"|rgb(177,124,92)
|
|-
|244
|muscles of abdominal wall
|style="background:rgb(171,85,68)"|rgb(171,85,68)
|
|-
|245
|skeleton of abdomen
|style="background:rgb(217,198,131)"|rgb(217,198,131)
|
|-
|246
|lumbar vertebral column
|style="background:rgb(212,188,102)"|rgb(212,188,102)
|
|-
|247
|female external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|248
|male external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|249
|skeleton of upper limb
|style="background:rgb(198,175,125)"|rgb(198,175,125)
|
|-
|250
|muscles of upper limb
|style="background:rgb(194,98,79)"|rgb(194,98,79)
|
|-
|251
|right upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|252
|left upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|253
|right shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|254
|left shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|255
|right arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|256
|left arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|257
|right elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|258
|left elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|259
|right forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|260
|left forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|261
|right wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|262
|left wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|263
|right hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|264
|left hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|265
|skeleton of lower limb
|style="background:rgb(255,238,170)"|rgb(255,238,170)
|
|-
|266
|muscles of lower limb
|style="background:rgb(206,111,93)"|rgb(206,111,93)
|
|-
|267
|right lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|268
|left lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|269
|right hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|270
|left hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|271
|right thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|272
|left thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|273
|right knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|274
|left knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|275
|right leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|276
|left leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|277
|right foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|278
|left foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|279
|peripheral nervous system
|style="background:rgb(216,186,0)"|rgb(216,186,0)
|
|-
|280
|autonomic nerve
|style="background:rgb(255,226,77)"|rgb(255,226,77)
|
|-
|281
|sympathetic trunk
|style="background:rgb(255,243,106)"|rgb(255,243,106)
|
|-
|282
|cranial nerves
|style="background:rgb(255,234,92)"|rgb(255,234,92)
|
|-
|283
|vagus nerve
|style="background:rgb(240,210,35)"|rgb(240,210,35)
|
|-
|284
|peripheral nerve
|style="background:rgb(224,194,0)"|rgb(224,194,0)
|
|-
|285
|circulatory system
|style="background:rgb(213,99,79)"|rgb(213,99,79)
|
|-
|286
|systemic arterial system
|style="background:rgb(217,102,81)"|rgb(217,102,81)
|
|-
|287
|systemic venous system
|style="background:rgb(0,147,202)"|rgb(0,147,202)
|
|-
|288
|pulmonary arterial system
|style="background:rgb(0,122,171)"|rgb(0,122,171)
|
|-
|289
|pulmonary venous system
|style="background:rgb(186,77,64)"|rgb(186,77,64)
|
|-
|290
|lymphatic system
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|291
|needle
|style="background:rgb(240,255,30)"|rgb(240,255,30)
|
|-
|292
|region 0
|style="background:rgb(185,232,61)"|rgb(185,232,61)
|
|-
|293
|region 1
|style="background:rgb(0,226,255)"|rgb(0,226,255)
|
|-
|294
|region 2
|style="background:rgb(251,159,255)"|rgb(251,159,255)
|
|-
|295
|region 3
|style="background:rgb(230,169,29)"|rgb(230,169,29)
|
|-
|296
|region 4
|style="background:rgb(0,194,113)"|rgb(0,194,113)
|
|-
|297
|region 5
|style="background:rgb(104,160,249)"|rgb(104,160,249)
|
|-
|298
|region 6
|style="background:rgb(221,108,158)"|rgb(221,108,158)
|
|-
|299
|region 7
|style="background:rgb(137,142,0)"|rgb(137,142,0)
|
|-
|300
|region 8
|style="background:rgb(230,70,0)"|rgb(230,70,0)
|
|-
|301
|region 9
|style="background:rgb(0,147,0)"|rgb(0,147,0)
|
|-
|302
|region 10
|style="background:rgb(0,147,248)"|rgb(0,147,248)
|
|-
|303
|region 11
|style="background:rgb(231,0,206)"|rgb(231,0,206)
|
|-
|304
|region 12
|style="background:rgb(129,78,0)"|rgb(129,78,0)
|
|-
|305
|region 13
|style="background:rgb(0,116,0)"|rgb(0,116,0)
|
|-
|306
|region 14
|style="background:rgb(0,0,255)"|rgb(0,0,255)
|
|-
|307
|region 15
|style="background:rgb(157,0,0)"|rgb(157,0,0)
|
|-
|308
|unknown
|style="background:rgb(100,100,130)"|rgb(100,100,130)
|
|-
|309
|cyst
|style="background:rgb(205,205,100)"|rgb(205,205,100)
|
|-
|}

Documentation/4.1/SlicerApplication/LookupTables/TractographyColors

2012-08-07T14:21:44Z

Demian:

{{documentation/{{documentation/version}}/TractographyColors}}


*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].

This is the look-up table for the parcellation of the white matter of the brain.
*Authors: Ron Kikinis, Demian Wassermann, Marianna Jakab

==Lookup table==

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|background
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|
|-
|1
|CC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Corpus Callosum
|-
|2
|CC genu
|style="background:rgb(241,214,145)"|rgb(241,214,145)
|Genu of the Corpus Callosum
|-
|3
|CC body
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|Body of the Corpus Callosum
|-
|4
|CC splenium
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|Splenium of the Corpus Callosum
|-
|5
|r AC
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right arcuate fasciculus
|-
|6
|l AC
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|left arcuate fasciculus
|-
|7
|r IOFF
|style="background:rgb(144,238,144)"|rgb(144,238,144)
|right inferior occipito-frontal fasciculus
|-
|8
|l IOFF
|style="background:rgb(192,104,88)"|rgb(192,104,88)
|left inferior occipito-frontal fasciculus
|-
|9
|r ILF
|style="background:rgb(220,245,20)"|rgb(220,245,20)
|right inferior longitudinal fasciculus
|-
|10
|l ILF
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left inferior longitudinal fasciculus
|-
|11
|r UNC
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|right uncinate fasciculus
|-
|12
|l UNC
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|left uncinate fasciculus
|-
|13
|r CST
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|right cortico-spinal tract
|-
|14
|l CST
|style="background:rgb(250,250,210)"|rgb(250,250,210)
|left cortico-spinal tract
|-
|15
|r OR
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right optic radiation
|-
|16
|l OR
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|left optic radiation
|-
|17
|r CB
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right cingulate bundle
|-
|18
|l CB
|style="background:rgb(183,156,220)"|rgb(183,156,220)
|left cingulate bundle
|-
|19
|r SLF 1
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|right superior longitudinal fasciculus 1
|-
|20
|l SLF 1
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|left superior longitudinal fasciculus 1
|-
|21
|r SLF 2
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|right superior longitudinal fasciculus 2
|-
|22
|l SLF 2
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|left superior longitudinal fasciculus 2
|-
|23
|r SLF 3
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|right superior longitudinal fasciculus 3
|-
|24
|l SLF 3
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|left superior longitudinal fasciculus 3
|-
|25
|r MDLF
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|right middle longitudinal fasciculus
|-
|26
|l MDLF
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|left middle longitudinal fasciculus
|-
|27
|r EC
|style="background:rgb(214,230,130)"|rgb(214,230,130)
|right extreme capsule
|-
|28
|l EC
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left extreme capsule
|-
|29
|DHC
|style="background:rgb(218,255,255)"|rgb(218,255,255)
|Dorsal hippocampal comissure
|-
|30
|AnC
|style="background:rgb(170,250,250)"|rgb(170,250,250)
|Anterior Comissure
|-
|31
|FC
|style="background:rgb(140,224,228)"|rgb(140,224,228)
|Forniceal Comissure
|-
|32
|r SOFF
|style="background:rgb(188,65,28)"|rgb(188,65,28)
|right superior occipito-frontal fasciculus
|-
|33
|l SOFF
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|left superior occipito-frontal fasciculus
|-
|34
|l CT
|style="background:rgb(145,60,66)"|rgb(145,60,66)
|left cortico-thalamical pathways
|-
|35
|r CT
|style="background:rgb(150,98,83)"|rgb(150,98,83)
|right cortico-thalamical pathways
|-
|36
|l SC
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|left cortico-striatal pathways
|-
|37
|r SC
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right cortico-striatal pathways
|-
|38
|l CP
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|left cortico-pontine projections
|-
|39
|r CP
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|right cortico-pontine projections
|-
|40
|PT
|style="background:rgb(68,131,98)"|rgb(68,131,98)
|Pontine Tract
|-
|41
|PC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Posterior comissure
|-
|42
|right frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|43
|left frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|44
|right temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|45
|left temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|46
|right parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|47
|left parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|48
|right occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|49
|left occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|50
|right insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|51
|left insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|52
|right limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|53
|left limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|54
|right striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|55
|left striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|56
|right caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|57
|left caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|58
|right putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|59
|left putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|60
|right pullidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|61
|left pallidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|62
|right amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|63
|left amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|64
|diencephalon
|style="background:rgb(69,110,53)"|rgb(69,110,53)
|
|-
|65
|thalamus
|style="background:rgb(166,113,137)"|rgb(166,113,137)
|
|-
|66
|right thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|67
|left thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|68
|pineal gland
|style="background:rgb(253,135,192)"|rgb(253,135,192)
|
|-
|69
|midbrain
|style="background:rgb(145,92,109)"|rgb(145,92,109)
|
|-
|70
|substantia nigra
|style="background:rgb(46,101,131)"|rgb(46,101,131)
|
|-
|71
|right substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|72
|left substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|73
|cerebral white matter
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|74
|right superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|75
|left superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|76
|right inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|77
|left inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|78
|right arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|79
|left arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|80
|right uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|81
|left uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|82
|right cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|83
|left cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|84
|projection fibers
|style="background:rgb(126,126,55)"|rgb(126,126,55)
|
|-
|85
|right corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|86
|left corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|87
|right optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|88
|left optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|89
|right medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|90
|left medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|91
|right superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|92
|left superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|93
|right middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|94
|left middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|95
|right inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|96
|left inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|97
|optic chiasm
|style="background:rgb(99,106,24)"|rgb(99,106,24)
|
|-
|98
|right optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|99
|left optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|100
|right fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|101
|left fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|102
|commissural fibers
|style="background:rgb(138,95,74)"|rgb(138,95,74)
|
|-
|103
|corpus callosum
|style="background:rgb(97,113,158)"|rgb(97,113,158)
|
|-
|104
|posterior commissure
|style="background:rgb(126,161,197)"|rgb(126,161,197)
|
|-
|105
|cerebellar white matter
|style="background:rgb(194,195,164)"|rgb(194,195,164)
|
|-
|106
|CSF space
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|107
|ventricles of brain
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|108
|right lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|109
|left lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|110
|right third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|111
|left third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|112
|cerebral aqueduct
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|113
|fourth ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|114
|subarachnoid space
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|115
|spinal cord
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|116
|gray matter of spinal cord
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|117
|white matter of spinal cord
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|118
|endocrine system of brain
|style="background:rgb(82,174,128)"|rgb(82,174,128)
|
|-
|119
|pituitary gland
|style="background:rgb(57,157,110)"|rgb(57,157,110)
|
|-
|120
|adenohypophysis
|style="background:rgb(60,143,83)"|rgb(60,143,83)
|
|-
|121
|neurohypophysis
|style="background:rgb(92,162,109)"|rgb(92,162,109)
|
|-
|122
|meninges
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|123
|dura mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|124
|arachnoid
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|125
|pia mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|126
|muscles of head
|style="background:rgb(201,121,77)"|rgb(201,121,77)
|
|-
|127
|salivary glands
|style="background:rgb(70,163,117)"|rgb(70,163,117)
|
|-
|128
|lips
|style="background:rgb(188,91,95)"|rgb(188,91,95)
|
|-
|129
|nose
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|130
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|131
|soft palate
|style="background:rgb(182,105,107)"|rgb(182,105,107)
|
|-
|132
|right inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|133
|left inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|134
|right external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|135
|left external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|136
|right middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|137
|left middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|138
|right eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|139
|left eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|140
|skull
|style="background:rgb(241,213,144)"|rgb(241,213,144)
|
|-
|141
|right frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|142
|left frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|143
|right parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|144
|left parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|145
|right temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|146
|left temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|147
|right sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|148
|left sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|149
|right ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|150
|left ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|151
|occipital bone
|style="background:rgb(255,230,138)"|rgb(255,230,138)
|
|-
|152
|maxilla
|style="background:rgb(196,172,68)"|rgb(196,172,68)
|
|-
|153
|right zygomatic bone
|style="background:rgb(255,255,167)"|rgb(255,255,167)
|
|-
|154
|right lacrimal bone
|style="background:rgb(255,250,160)"|rgb(255,250,160)
|
|-
|155
|vomer bone
|style="background:rgb(255,237,145)"|rgb(255,237,145)
|
|-
|156
|right palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|157
|left palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|158
|mandible
|style="background:rgb(222,198,101)"|rgb(222,198,101)
|
|-
|159
|neck
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|160
|muscles of neck
|style="background:rgb(213,124,109)"|rgb(213,124,109)
|
|-
|161
|pharynx
|style="background:rgb(184,105,108)"|rgb(184,105,108)
|
|-
|162
|larynx
|style="background:rgb(150,208,243)"|rgb(150,208,243)
|
|-
|163
|thyroid gland
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|164
|right parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|165
|left parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|166
|skeleton of neck
|style="background:rgb(242,206,142)"|rgb(242,206,142)
|
|-
|167
|hyoid bone
|style="background:rgb(250,210,139)"|rgb(250,210,139)
|
|-
|168
|cervical vertebral column
|style="background:rgb(255,255,207)"|rgb(255,255,207)
|
|-
|169
|thorax
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|170
|trachea
|style="background:rgb(182,228,255)"|rgb(182,228,255)
|
|-
|171
|bronchi
|style="background:rgb(175,216,244)"|rgb(175,216,244)
|
|-
|172
|right lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|173
|left lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|174
|superior lobe of right lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|175
|superior lobe of left lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|176
|middle lobe of right lung
|style="background:rgb(202,164,140)"|rgb(202,164,140)
|
|-
|177
|inferior lobe of right lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|178
|inferior lobe of left lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|179
|pleura
|style="background:rgb(255,245,217)"|rgb(255,245,217)
|
|-
|180
|heart
|style="background:rgb(206,110,84)"|rgb(206,110,84)
|
|-
|181
|right atrium
|style="background:rgb(210,115,89)"|rgb(210,115,89)
|
|-
|182
|left atrium
|style="background:rgb(203,108,81)"|rgb(203,108,81)
|
|-
|183
|atrial septum
|style="background:rgb(233,138,112)"|rgb(233,138,112)
|
|-
|184
|ventricular septum
|style="background:rgb(195,100,73)"|rgb(195,100,73)
|
|-
|185
|right ventricle of heart
|style="background:rgb(181,85,57)"|rgb(181,85,57)
|
|-
|186
|left ventricle of heart
|style="background:rgb(152,55,13)"|rgb(152,55,13)
|
|-
|187
|mitral valve
|style="background:rgb(159,63,27)"|rgb(159,63,27)
|
|-
|188
|tricuspid valve
|style="background:rgb(166,70,38)"|rgb(166,70,38)
|
|-
|189
|aortic valve
|style="background:rgb(218,123,97)"|rgb(218,123,97)
|
|-
|190
|pulmonary valve
|style="background:rgb(225,130,104)"|rgb(225,130,104)
|
|-
|191
|aorta
|style="background:rgb(224,97,76)"|rgb(224,97,76)
|
|-
|192
|pericardium
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|193
|pericardial cavity
|style="background:rgb(184,122,154)"|rgb(184,122,154)
|
|-
|194
|esophagus
|style="background:rgb(211,171,143)"|rgb(211,171,143)
|
|-
|195
|thymus
|style="background:rgb(47,150,103)"|rgb(47,150,103)
|
|-
|196
|mediastinum
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|197
|skin of thoracic wall
|style="background:rgb(173,121,88)"|rgb(173,121,88)
|
|-
|198
|muscles of thoracic wall
|style="background:rgb(188,95,76)"|rgb(188,95,76)
|
|-
|199
|skeleton of thorax
|style="background:rgb(255,239,172)"|rgb(255,239,172)
|
|-
|200
|thoracic vertebral column
|style="background:rgb(226,202,134)"|rgb(226,202,134)
|
|-
|201
|ribs
|style="background:rgb(253,232,158)"|rgb(253,232,158)
|
|-
|202
|sternum
|style="background:rgb(244,217,154)"|rgb(244,217,154)
|
|-
|203
|right clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|204
|left clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|205
|abdominal cavity
|style="background:rgb(186,124,161)"|rgb(186,124,161)
|
|-
|206
|abdomen
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|207
|peritoneum
|style="background:rgb(255,255,220)"|rgb(255,255,220)
|
|-
|208
|omentum
|style="background:rgb(234,234,194)"|rgb(234,234,194)
|
|-
|209
|peritoneal cavity
|style="background:rgb(204,142,178)"|rgb(204,142,178)
|
|-
|210
|retroperitoneal space
|style="background:rgb(180,119,153)"|rgb(180,119,153)
|
|-
|211
|stomach
|style="background:rgb(216,132,105)"|rgb(216,132,105)
|
|-
|212
|duodenum
|style="background:rgb(255,253,229)"|rgb(255,253,229)
|
|-
|213
|small bowel
|style="background:rgb(205,167,142)"|rgb(205,167,142)
|
|-
|214
|colon
|style="background:rgb(204,168,143)"|rgb(204,168,143)
|
|-
|215
|anus
|style="background:rgb(255,224,199)"|rgb(255,224,199)
|
|-
|216
|liver
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|217
|biliary tree
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|218
|gallbladder
|style="background:rgb(139,150,98)"|rgb(139,150,98)
|
|-
|219
|pancreas
|style="background:rgb(249,180,111)"|rgb(249,180,111)
|
|-
|220
|spleen
|style="background:rgb(157,108,162)"|rgb(157,108,162)
|
|-
|221
|urinary system
|style="background:rgb(203,136,116)"|rgb(203,136,116)
|
|-
|222
|right kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|223
|left kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|224
|right ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|225
|left ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|226
|urinary bladder
|style="background:rgb(222,154,132)"|rgb(222,154,132)
|
|-
|227
|urethra
|style="background:rgb(124,186,223)"|rgb(124,186,223)
|
|-
|228
|right adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|229
|left adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|230
|female internal genitalia
|style="background:rgb(244,170,147)"|rgb(244,170,147)
|
|-
|231
|uterus
|style="background:rgb(255,181,158)"|rgb(255,181,158)
|
|-
|232
|right fallopian tube
|style="background:rgb(255,190,165)"|rgb(255,190,165)
|
|-
|233
|left fallopian tube
|style="background:rgb(227,153,130)"|rgb(227,153,130)
|
|-
|234
|right ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|235
|left ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|236
|vagina
|style="background:rgb(193,123,103)"|rgb(193,123,103)
|
|-
|237
|male internal genitalia
|style="background:rgb(216,146,127)"|rgb(216,146,127)
|
|-
|238
|prostate
|style="background:rgb(230,158,140)"|rgb(230,158,140)
|
|-
|239
|right seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|240
|left seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|241
|right deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|242
|left deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|243
|skin of abdominal wall
|style="background:rgb(177,124,92)"|rgb(177,124,92)
|
|-
|244
|muscles of abdominal wall
|style="background:rgb(171,85,68)"|rgb(171,85,68)
|
|-
|245
|skeleton of abdomen
|style="background:rgb(217,198,131)"|rgb(217,198,131)
|
|-
|246
|lumbar vertebral column
|style="background:rgb(212,188,102)"|rgb(212,188,102)
|
|-
|247
|female external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|248
|male external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|249
|skeleton of upper limb
|style="background:rgb(198,175,125)"|rgb(198,175,125)
|
|-
|250
|muscles of upper limb
|style="background:rgb(194,98,79)"|rgb(194,98,79)
|
|-
|251
|right upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|252
|left upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|253
|right shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|254
|left shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|255
|right arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|256
|left arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|257
|right elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|258
|left elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|259
|right forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|260
|left forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|261
|right wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|262
|left wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|263
|right hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|264
|left hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|265
|skeleton of lower limb
|style="background:rgb(255,238,170)"|rgb(255,238,170)
|
|-
|266
|muscles of lower limb
|style="background:rgb(206,111,93)"|rgb(206,111,93)
|
|-
|267
|right lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|268
|left lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|269
|right hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|270
|left hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|271
|right thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|272
|left thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|273
|right knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|274
|left knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|275
|right leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|276
|left leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|277
|right foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|278
|left foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|279
|peripheral nervous system
|style="background:rgb(216,186,0)"|rgb(216,186,0)
|
|-
|280
|autonomic nerve
|style="background:rgb(255,226,77)"|rgb(255,226,77)
|
|-
|281
|sympathetic trunk
|style="background:rgb(255,243,106)"|rgb(255,243,106)
|
|-
|282
|cranial nerves
|style="background:rgb(255,234,92)"|rgb(255,234,92)
|
|-
|283
|vagus nerve
|style="background:rgb(240,210,35)"|rgb(240,210,35)
|
|-
|284
|peripheral nerve
|style="background:rgb(224,194,0)"|rgb(224,194,0)
|
|-
|285
|circulatory system
|style="background:rgb(213,99,79)"|rgb(213,99,79)
|
|-
|286
|systemic arterial system
|style="background:rgb(217,102,81)"|rgb(217,102,81)
|
|-
|287
|systemic venous system
|style="background:rgb(0,147,202)"|rgb(0,147,202)
|
|-
|288
|pulmonary arterial system
|style="background:rgb(0,122,171)"|rgb(0,122,171)
|
|-
|289
|pulmonary venous system
|style="background:rgb(186,77,64)"|rgb(186,77,64)
|
|-
|290
|lymphatic system
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|291
|needle
|style="background:rgb(240,255,30)"|rgb(240,255,30)
|
|-
|292
|region 0
|style="background:rgb(185,232,61)"|rgb(185,232,61)
|
|-
|293
|region 1
|style="background:rgb(0,226,255)"|rgb(0,226,255)
|
|-
|294
|region 2
|style="background:rgb(251,159,255)"|rgb(251,159,255)
|
|-
|295
|region 3
|style="background:rgb(230,169,29)"|rgb(230,169,29)
|
|-
|296
|region 4
|style="background:rgb(0,194,113)"|rgb(0,194,113)
|
|-
|297
|region 5
|style="background:rgb(104,160,249)"|rgb(104,160,249)
|
|-
|298
|region 6
|style="background:rgb(221,108,158)"|rgb(221,108,158)
|
|-
|299
|region 7
|style="background:rgb(137,142,0)"|rgb(137,142,0)
|
|-
|300
|region 8
|style="background:rgb(230,70,0)"|rgb(230,70,0)
|
|-
|301
|region 9
|style="background:rgb(0,147,0)"|rgb(0,147,0)
|
|-
|302
|region 10
|style="background:rgb(0,147,248)"|rgb(0,147,248)
|
|-
|303
|region 11
|style="background:rgb(231,0,206)"|rgb(231,0,206)
|
|-
|304
|region 12
|style="background:rgb(129,78,0)"|rgb(129,78,0)
|
|-
|305
|region 13
|style="background:rgb(0,116,0)"|rgb(0,116,0)
|
|-
|306
|region 14
|style="background:rgb(0,0,255)"|rgb(0,0,255)
|
|-
|307
|region 15
|style="background:rgb(157,0,0)"|rgb(157,0,0)
|
|-
|308
|unknown
|style="background:rgb(100,100,130)"|rgb(100,100,130)
|
|-
|309
|cyst
|style="background:rgb(205,205,100)"|rgb(205,205,100)
|
|-
|}

Documentation/4.1/SlicerApplication/LookupTables/TractographyColors

2012-08-07T14:08:49Z

Demian:

{{documentation/{{documentation/version}}/TractographyColors}}


*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].

This is the look-up table for the parcellation of the white matter of the brain.
*Authors: Ron Kikinis, Demian Wassermann, Marianna Jakab

==Lookup table==

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|background
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|
|-
|1
|CC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Corpus Callosum
|-
|2
|CC genu
|style="background:rgb(241,214,145)"|rgb(241,214,145)
|Genu of the Corpus Callosum
|-
|3
|CC body
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|Body of the Corpus Callosum
|-
|4
|CC splenium
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|Splenium of the Corpus Callosum
|-
|5
|r AC
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right arcuate fasciculus
|-
|6
|l AC
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|left arcuate fasciculus
|-
|7
|r IFOF
|style="background:rgb(144,238,144)"|rgb(144,238,144)
|right inferior fronto-occipital fasciculus
|-
|8
|l IFOF
|style="background:rgb(192,104,88)"|rgb(192,104,88)
|left inferior fronto-occipital fasciculus
|-
|9
|r ILF
|style="background:rgb(220,245,20)"|rgb(220,245,20)
|right inferior longitudinal fasciculus
|-
|10
|l ILF
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left inferior longitudinal fasciculus
|-
|11
|r UNC
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|right uncinate fasciculus
|-
|12
|l UNC
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|left uncinate fasciculus
|-
|13
|r CST
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|right cortico-spinal tract
|-
|14
|l CST
|style="background:rgb(250,250,210)"|rgb(250,250,210)
|left cortico-spinal tract
|-
|15
|r OR
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right optic radiation
|-
|16
|l OR
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|left optic radiation
|-
|17
|r CB
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right cingulate bundle
|-
|18
|l CB
|style="background:rgb(183,156,220)"|rgb(183,156,220)
|left cingulate bundle
|-
|19
|r SLF 1
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|right superior longitudinal fasciculus 1
|-
|20
|l SLF 1
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|left superior longitudinal fasciculus 1
|-
|21
|r SLF 2
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|right superior longitudinal fasciculus 2
|-
|22
|l SLF 2
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|left superior longitudinal fasciculus 2
|-
|23
|r SLF 3
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|right superior longitudinal fasciculus 3
|-
|24
|l SLF 3
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|left superior longitudinal fasciculus 3
|-
|25
|r MDLF
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|right middle longitudinal fasciculus
|-
|26
|r MDLF
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|r middle longitudinal fasciculus
|-
|27
|urine
|style="background:rgb(214,230,130)"|rgb(214,230,130)
|
|-
|28
|feces
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|
|-
|29
|gas
|style="background:rgb(218,255,255)"|rgb(218,255,255)
|
|-
|30
|fluid
|style="background:rgb(170,250,250)"|rgb(170,250,250)
|
|-
|31
|edema
|style="background:rgb(140,224,228)"|rgb(140,224,228)
|
|-
|32
|bleeding
|style="background:rgb(188,65,28)"|rgb(188,65,28)
|
|-
|33
|necrosis
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|
|-
|34
|clot
|style="background:rgb(145,60,66)"|rgb(145,60,66)
|
|-
|35
|embolism
|style="background:rgb(150,98,83)"|rgb(150,98,83)
|
|-
|36
|head
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|37
|central nervous system
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|38
|brain
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|39
|gray matter of brain
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|40
|telencephalon
|style="background:rgb(68,131,98)"|rgb(68,131,98)
|
|-
|41
|cerebral cortex
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|
|-
|42
|right frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|43
|left frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|44
|right temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|45
|left temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|46
|right parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|47
|left parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|48
|right occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|49
|left occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|50
|right insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|51
|left insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|52
|right limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|53
|left limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|54
|right striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|55
|left striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|56
|right caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|57
|left caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|58
|right putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|59
|left putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|60
|right pullidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|61
|left pallidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|62
|right amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|63
|left amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|64
|diencephalon
|style="background:rgb(69,110,53)"|rgb(69,110,53)
|
|-
|65
|thalamus
|style="background:rgb(166,113,137)"|rgb(166,113,137)
|
|-
|66
|right thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|67
|left thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|68
|pineal gland
|style="background:rgb(253,135,192)"|rgb(253,135,192)
|
|-
|69
|midbrain
|style="background:rgb(145,92,109)"|rgb(145,92,109)
|
|-
|70
|substantia nigra
|style="background:rgb(46,101,131)"|rgb(46,101,131)
|
|-
|71
|right substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|72
|left substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|73
|cerebral white matter
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|74
|right superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|75
|left superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|76
|right inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|77
|left inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|78
|right arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|79
|left arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|80
|right uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|81
|left uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|82
|right cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|83
|left cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|84
|projection fibers
|style="background:rgb(126,126,55)"|rgb(126,126,55)
|
|-
|85
|right corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|86
|left corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|87
|right optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|88
|left optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|89
|right medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|90
|left medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|91
|right superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|92
|left superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|93
|right middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|94
|left middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|95
|right inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|96
|left inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|97
|optic chiasm
|style="background:rgb(99,106,24)"|rgb(99,106,24)
|
|-
|98
|right optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|99
|left optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|100
|right fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|101
|left fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|102
|commissural fibers
|style="background:rgb(138,95,74)"|rgb(138,95,74)
|
|-
|103
|corpus callosum
|style="background:rgb(97,113,158)"|rgb(97,113,158)
|
|-
|104
|posterior commissure
|style="background:rgb(126,161,197)"|rgb(126,161,197)
|
|-
|105
|cerebellar white matter
|style="background:rgb(194,195,164)"|rgb(194,195,164)
|
|-
|106
|CSF space
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|107
|ventricles of brain
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|108
|right lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|109
|left lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|110
|right third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|111
|left third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|112
|cerebral aqueduct
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|113
|fourth ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|114
|subarachnoid space
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|115
|spinal cord
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|116
|gray matter of spinal cord
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|117
|white matter of spinal cord
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|118
|endocrine system of brain
|style="background:rgb(82,174,128)"|rgb(82,174,128)
|
|-
|119
|pituitary gland
|style="background:rgb(57,157,110)"|rgb(57,157,110)
|
|-
|120
|adenohypophysis
|style="background:rgb(60,143,83)"|rgb(60,143,83)
|
|-
|121
|neurohypophysis
|style="background:rgb(92,162,109)"|rgb(92,162,109)
|
|-
|122
|meninges
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|123
|dura mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|124
|arachnoid
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|125
|pia mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|126
|muscles of head
|style="background:rgb(201,121,77)"|rgb(201,121,77)
|
|-
|127
|salivary glands
|style="background:rgb(70,163,117)"|rgb(70,163,117)
|
|-
|128
|lips
|style="background:rgb(188,91,95)"|rgb(188,91,95)
|
|-
|129
|nose
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|130
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|131
|soft palate
|style="background:rgb(182,105,107)"|rgb(182,105,107)
|
|-
|132
|right inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|133
|left inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|134
|right external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|135
|left external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|136
|right middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|137
|left middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|138
|right eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|139
|left eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|140
|skull
|style="background:rgb(241,213,144)"|rgb(241,213,144)
|
|-
|141
|right frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|142
|left frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|143
|right parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|144
|left parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|145
|right temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|146
|left temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|147
|right sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|148
|left sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|149
|right ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|150
|left ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|151
|occipital bone
|style="background:rgb(255,230,138)"|rgb(255,230,138)
|
|-
|152
|maxilla
|style="background:rgb(196,172,68)"|rgb(196,172,68)
|
|-
|153
|right zygomatic bone
|style="background:rgb(255,255,167)"|rgb(255,255,167)
|
|-
|154
|right lacrimal bone
|style="background:rgb(255,250,160)"|rgb(255,250,160)
|
|-
|155
|vomer bone
|style="background:rgb(255,237,145)"|rgb(255,237,145)
|
|-
|156
|right palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|157
|left palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|158
|mandible
|style="background:rgb(222,198,101)"|rgb(222,198,101)
|
|-
|159
|neck
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|160
|muscles of neck
|style="background:rgb(213,124,109)"|rgb(213,124,109)
|
|-
|161
|pharynx
|style="background:rgb(184,105,108)"|rgb(184,105,108)
|
|-
|162
|larynx
|style="background:rgb(150,208,243)"|rgb(150,208,243)
|
|-
|163
|thyroid gland
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|164
|right parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|165
|left parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|166
|skeleton of neck
|style="background:rgb(242,206,142)"|rgb(242,206,142)
|
|-
|167
|hyoid bone
|style="background:rgb(250,210,139)"|rgb(250,210,139)
|
|-
|168
|cervical vertebral column
|style="background:rgb(255,255,207)"|rgb(255,255,207)
|
|-
|169
|thorax
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|170
|trachea
|style="background:rgb(182,228,255)"|rgb(182,228,255)
|
|-
|171
|bronchi
|style="background:rgb(175,216,244)"|rgb(175,216,244)
|
|-
|172
|right lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|173
|left lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|174
|superior lobe of right lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|175
|superior lobe of left lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|176
|middle lobe of right lung
|style="background:rgb(202,164,140)"|rgb(202,164,140)
|
|-
|177
|inferior lobe of right lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|178
|inferior lobe of left lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|179
|pleura
|style="background:rgb(255,245,217)"|rgb(255,245,217)
|
|-
|180
|heart
|style="background:rgb(206,110,84)"|rgb(206,110,84)
|
|-
|181
|right atrium
|style="background:rgb(210,115,89)"|rgb(210,115,89)
|
|-
|182
|left atrium
|style="background:rgb(203,108,81)"|rgb(203,108,81)
|
|-
|183
|atrial septum
|style="background:rgb(233,138,112)"|rgb(233,138,112)
|
|-
|184
|ventricular septum
|style="background:rgb(195,100,73)"|rgb(195,100,73)
|
|-
|185
|right ventricle of heart
|style="background:rgb(181,85,57)"|rgb(181,85,57)
|
|-
|186
|left ventricle of heart
|style="background:rgb(152,55,13)"|rgb(152,55,13)
|
|-
|187
|mitral valve
|style="background:rgb(159,63,27)"|rgb(159,63,27)
|
|-
|188
|tricuspid valve
|style="background:rgb(166,70,38)"|rgb(166,70,38)
|
|-
|189
|aortic valve
|style="background:rgb(218,123,97)"|rgb(218,123,97)
|
|-
|190
|pulmonary valve
|style="background:rgb(225,130,104)"|rgb(225,130,104)
|
|-
|191
|aorta
|style="background:rgb(224,97,76)"|rgb(224,97,76)
|
|-
|192
|pericardium
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|193
|pericardial cavity
|style="background:rgb(184,122,154)"|rgb(184,122,154)
|
|-
|194
|esophagus
|style="background:rgb(211,171,143)"|rgb(211,171,143)
|
|-
|195
|thymus
|style="background:rgb(47,150,103)"|rgb(47,150,103)
|
|-
|196
|mediastinum
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|197
|skin of thoracic wall
|style="background:rgb(173,121,88)"|rgb(173,121,88)
|
|-
|198
|muscles of thoracic wall
|style="background:rgb(188,95,76)"|rgb(188,95,76)
|
|-
|199
|skeleton of thorax
|style="background:rgb(255,239,172)"|rgb(255,239,172)
|
|-
|200
|thoracic vertebral column
|style="background:rgb(226,202,134)"|rgb(226,202,134)
|
|-
|201
|ribs
|style="background:rgb(253,232,158)"|rgb(253,232,158)
|
|-
|202
|sternum
|style="background:rgb(244,217,154)"|rgb(244,217,154)
|
|-
|203
|right clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|204
|left clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|205
|abdominal cavity
|style="background:rgb(186,124,161)"|rgb(186,124,161)
|
|-
|206
|abdomen
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|207
|peritoneum
|style="background:rgb(255,255,220)"|rgb(255,255,220)
|
|-
|208
|omentum
|style="background:rgb(234,234,194)"|rgb(234,234,194)
|
|-
|209
|peritoneal cavity
|style="background:rgb(204,142,178)"|rgb(204,142,178)
|
|-
|210
|retroperitoneal space
|style="background:rgb(180,119,153)"|rgb(180,119,153)
|
|-
|211
|stomach
|style="background:rgb(216,132,105)"|rgb(216,132,105)
|
|-
|212
|duodenum
|style="background:rgb(255,253,229)"|rgb(255,253,229)
|
|-
|213
|small bowel
|style="background:rgb(205,167,142)"|rgb(205,167,142)
|
|-
|214
|colon
|style="background:rgb(204,168,143)"|rgb(204,168,143)
|
|-
|215
|anus
|style="background:rgb(255,224,199)"|rgb(255,224,199)
|
|-
|216
|liver
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|217
|biliary tree
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|218
|gallbladder
|style="background:rgb(139,150,98)"|rgb(139,150,98)
|
|-
|219
|pancreas
|style="background:rgb(249,180,111)"|rgb(249,180,111)
|
|-
|220
|spleen
|style="background:rgb(157,108,162)"|rgb(157,108,162)
|
|-
|221
|urinary system
|style="background:rgb(203,136,116)"|rgb(203,136,116)
|
|-
|222
|right kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|223
|left kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|224
|right ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|225
|left ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|226
|urinary bladder
|style="background:rgb(222,154,132)"|rgb(222,154,132)
|
|-
|227
|urethra
|style="background:rgb(124,186,223)"|rgb(124,186,223)
|
|-
|228
|right adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|229
|left adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|230
|female internal genitalia
|style="background:rgb(244,170,147)"|rgb(244,170,147)
|
|-
|231
|uterus
|style="background:rgb(255,181,158)"|rgb(255,181,158)
|
|-
|232
|right fallopian tube
|style="background:rgb(255,190,165)"|rgb(255,190,165)
|
|-
|233
|left fallopian tube
|style="background:rgb(227,153,130)"|rgb(227,153,130)
|
|-
|234
|right ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|235
|left ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|236
|vagina
|style="background:rgb(193,123,103)"|rgb(193,123,103)
|
|-
|237
|male internal genitalia
|style="background:rgb(216,146,127)"|rgb(216,146,127)
|
|-
|238
|prostate
|style="background:rgb(230,158,140)"|rgb(230,158,140)
|
|-
|239
|right seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|240
|left seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|241
|right deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|242
|left deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|243
|skin of abdominal wall
|style="background:rgb(177,124,92)"|rgb(177,124,92)
|
|-
|244
|muscles of abdominal wall
|style="background:rgb(171,85,68)"|rgb(171,85,68)
|
|-
|245
|skeleton of abdomen
|style="background:rgb(217,198,131)"|rgb(217,198,131)
|
|-
|246
|lumbar vertebral column
|style="background:rgb(212,188,102)"|rgb(212,188,102)
|
|-
|247
|female external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|248
|male external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|249
|skeleton of upper limb
|style="background:rgb(198,175,125)"|rgb(198,175,125)
|
|-
|250
|muscles of upper limb
|style="background:rgb(194,98,79)"|rgb(194,98,79)
|
|-
|251
|right upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|252
|left upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|253
|right shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|254
|left shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|255
|right arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|256
|left arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|257
|right elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|258
|left elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|259
|right forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|260
|left forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|261
|right wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|262
|left wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|263
|right hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|264
|left hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|265
|skeleton of lower limb
|style="background:rgb(255,238,170)"|rgb(255,238,170)
|
|-
|266
|muscles of lower limb
|style="background:rgb(206,111,93)"|rgb(206,111,93)
|
|-
|267
|right lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|268
|left lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|269
|right hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|270
|left hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|271
|right thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|272
|left thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|273
|right knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|274
|left knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|275
|right leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|276
|left leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|277
|right foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|278
|left foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|279
|peripheral nervous system
|style="background:rgb(216,186,0)"|rgb(216,186,0)
|
|-
|280
|autonomic nerve
|style="background:rgb(255,226,77)"|rgb(255,226,77)
|
|-
|281
|sympathetic trunk
|style="background:rgb(255,243,106)"|rgb(255,243,106)
|
|-
|282
|cranial nerves
|style="background:rgb(255,234,92)"|rgb(255,234,92)
|
|-
|283
|vagus nerve
|style="background:rgb(240,210,35)"|rgb(240,210,35)
|
|-
|284
|peripheral nerve
|style="background:rgb(224,194,0)"|rgb(224,194,0)
|
|-
|285
|circulatory system
|style="background:rgb(213,99,79)"|rgb(213,99,79)
|
|-
|286
|systemic arterial system
|style="background:rgb(217,102,81)"|rgb(217,102,81)
|
|-
|287
|systemic venous system
|style="background:rgb(0,147,202)"|rgb(0,147,202)
|
|-
|288
|pulmonary arterial system
|style="background:rgb(0,122,171)"|rgb(0,122,171)
|
|-
|289
|pulmonary venous system
|style="background:rgb(186,77,64)"|rgb(186,77,64)
|
|-
|290
|lymphatic system
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|291
|needle
|style="background:rgb(240,255,30)"|rgb(240,255,30)
|
|-
|292
|region 0
|style="background:rgb(185,232,61)"|rgb(185,232,61)
|
|-
|293
|region 1
|style="background:rgb(0,226,255)"|rgb(0,226,255)
|
|-
|294
|region 2
|style="background:rgb(251,159,255)"|rgb(251,159,255)
|
|-
|295
|region 3
|style="background:rgb(230,169,29)"|rgb(230,169,29)
|
|-
|296
|region 4
|style="background:rgb(0,194,113)"|rgb(0,194,113)
|
|-
|297
|region 5
|style="background:rgb(104,160,249)"|rgb(104,160,249)
|
|-
|298
|region 6
|style="background:rgb(221,108,158)"|rgb(221,108,158)
|
|-
|299
|region 7
|style="background:rgb(137,142,0)"|rgb(137,142,0)
|
|-
|300
|region 8
|style="background:rgb(230,70,0)"|rgb(230,70,0)
|
|-
|301
|region 9
|style="background:rgb(0,147,0)"|rgb(0,147,0)
|
|-
|302
|region 10
|style="background:rgb(0,147,248)"|rgb(0,147,248)
|
|-
|303
|region 11
|style="background:rgb(231,0,206)"|rgb(231,0,206)
|
|-
|304
|region 12
|style="background:rgb(129,78,0)"|rgb(129,78,0)
|
|-
|305
|region 13
|style="background:rgb(0,116,0)"|rgb(0,116,0)
|
|-
|306
|region 14
|style="background:rgb(0,0,255)"|rgb(0,0,255)
|
|-
|307
|region 15
|style="background:rgb(157,0,0)"|rgb(157,0,0)
|
|-
|308
|unknown
|style="background:rgb(100,100,130)"|rgb(100,100,130)
|
|-
|309
|cyst
|style="background:rgb(205,205,100)"|rgb(205,205,100)
|
|-
|}

Documentation/4.1/SlicerApplication/LookupTables/TractographyColors

2012-08-07T14:05:09Z

Demian:

{{documentation/{{documentation/version}}/TractographyColors}}


*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].

This is the look-up table for the parcellation of the white matter of the brain.
*Authors: Ron Kikinis, Demian Wassermann, Marianna Jakab

==Lookup table==

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|background
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|
|-
|1
|CC
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|Corpus Callosum
|-
|2
|CC genu
|style="background:rgb(241,214,145)"|rgb(241,214,145)
|Genu of the Corpus Callosum
|-
|3
|CC body
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|Body of the Corpus Callosum
|-
|4
|CC splenium
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|Splenium of the Corpus Callosum
|-
|5
|r SLF
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right superior longitudinal fasciculus
|-
|6
|l SLF
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|left superior longitudinal fasciculus
|-
|7
|r IFOF
|style="background:rgb(144,238,144)"|rgb(144,238,144)
|right inferior fronto-occipital fasciculus
|-
|8
|l IFOF
|style="background:rgb(192,104,88)"|rgb(192,104,88)
|left inferior fronto-occipital fasciculus
|-
|9
|r ILF
|style="background:rgb(220,245,20)"|rgb(220,245,20)
|right inferior longitudinal fasciculus
|-
|10
|l ILF
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|left inferior longitudinal fasciculus
|-
|11
|r UNC
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|right uncinate fasciculus
|-
|12
|l UNC
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|left uncinate fasciculus
|-
|13
|r CST
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|right cortico-spinal tract
|-
|14
|l CST
|style="background:rgb(250,250,210)"|rgb(250,250,210)
|left cortico-spinal tract
|-
|15
|r OR
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|right optic radiation
|-
|16
|l OR
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|left optic radiation
|-
|17
|r CB
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|right cingulate bundle
|-
|18
|l CB
|style="background:rgb(183,156,220)"|rgb(183,156,220)
|left cingulate bundle
|-
|19
|r SLF 1
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|right superior longitudinal fasciculus 1
|-
|20
|l SLF 1
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|left superior longitudinal fasciculus 1
|-
|21
|r SLF 2
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|right superior longitudinal fasciculus 2
|-
|22
|l SLF 2
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|left superior longitudinal fasciculus 2
|-
|23
|r SLF 3
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|right superior longitudinal fasciculus 3
|-
|24
|l SLF 3
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|left superior longitudinal fasciculus 3
|-
|25
|cerebro-spinal fluid
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|26
|bile
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|27
|urine
|style="background:rgb(214,230,130)"|rgb(214,230,130)
|
|-
|28
|feces
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|
|-
|29
|gas
|style="background:rgb(218,255,255)"|rgb(218,255,255)
|
|-
|30
|fluid
|style="background:rgb(170,250,250)"|rgb(170,250,250)
|
|-
|31
|edema
|style="background:rgb(140,224,228)"|rgb(140,224,228)
|
|-
|32
|bleeding
|style="background:rgb(188,65,28)"|rgb(188,65,28)
|
|-
|33
|necrosis
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|
|-
|34
|clot
|style="background:rgb(145,60,66)"|rgb(145,60,66)
|
|-
|35
|embolism
|style="background:rgb(150,98,83)"|rgb(150,98,83)
|
|-
|36
|head
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|37
|central nervous system
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|38
|brain
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|39
|gray matter of brain
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|40
|telencephalon
|style="background:rgb(68,131,98)"|rgb(68,131,98)
|
|-
|41
|cerebral cortex
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|
|-
|42
|right frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|43
|left frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|44
|right temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|45
|left temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|46
|right parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|47
|left parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|48
|right occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|49
|left occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|50
|right insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|51
|left insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|52
|right limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|53
|left limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|54
|right striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|55
|left striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|56
|right caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|57
|left caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|58
|right putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|59
|left putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|60
|right pullidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|61
|left pallidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|62
|right amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|63
|left amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|64
|diencephalon
|style="background:rgb(69,110,53)"|rgb(69,110,53)
|
|-
|65
|thalamus
|style="background:rgb(166,113,137)"|rgb(166,113,137)
|
|-
|66
|right thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|67
|left thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|68
|pineal gland
|style="background:rgb(253,135,192)"|rgb(253,135,192)
|
|-
|69
|midbrain
|style="background:rgb(145,92,109)"|rgb(145,92,109)
|
|-
|70
|substantia nigra
|style="background:rgb(46,101,131)"|rgb(46,101,131)
|
|-
|71
|right substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|72
|left substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|73
|cerebral white matter
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|74
|right superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|75
|left superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|76
|right inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|77
|left inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|78
|right arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|79
|left arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|80
|right uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|81
|left uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|82
|right cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|83
|left cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|84
|projection fibers
|style="background:rgb(126,126,55)"|rgb(126,126,55)
|
|-
|85
|right corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|86
|left corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|87
|right optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|88
|left optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|89
|right medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|90
|left medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|91
|right superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|92
|left superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|93
|right middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|94
|left middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|95
|right inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|96
|left inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|97
|optic chiasm
|style="background:rgb(99,106,24)"|rgb(99,106,24)
|
|-
|98
|right optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|99
|left optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|100
|right fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|101
|left fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|102
|commissural fibers
|style="background:rgb(138,95,74)"|rgb(138,95,74)
|
|-
|103
|corpus callosum
|style="background:rgb(97,113,158)"|rgb(97,113,158)
|
|-
|104
|posterior commissure
|style="background:rgb(126,161,197)"|rgb(126,161,197)
|
|-
|105
|cerebellar white matter
|style="background:rgb(194,195,164)"|rgb(194,195,164)
|
|-
|106
|CSF space
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|107
|ventricles of brain
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|108
|right lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|109
|left lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|110
|right third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|111
|left third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|112
|cerebral aqueduct
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|113
|fourth ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|114
|subarachnoid space
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|115
|spinal cord
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|116
|gray matter of spinal cord
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|117
|white matter of spinal cord
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|118
|endocrine system of brain
|style="background:rgb(82,174,128)"|rgb(82,174,128)
|
|-
|119
|pituitary gland
|style="background:rgb(57,157,110)"|rgb(57,157,110)
|
|-
|120
|adenohypophysis
|style="background:rgb(60,143,83)"|rgb(60,143,83)
|
|-
|121
|neurohypophysis
|style="background:rgb(92,162,109)"|rgb(92,162,109)
|
|-
|122
|meninges
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|123
|dura mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|124
|arachnoid
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|125
|pia mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|126
|muscles of head
|style="background:rgb(201,121,77)"|rgb(201,121,77)
|
|-
|127
|salivary glands
|style="background:rgb(70,163,117)"|rgb(70,163,117)
|
|-
|128
|lips
|style="background:rgb(188,91,95)"|rgb(188,91,95)
|
|-
|129
|nose
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|130
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|131
|soft palate
|style="background:rgb(182,105,107)"|rgb(182,105,107)
|
|-
|132
|right inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|133
|left inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|134
|right external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|135
|left external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|136
|right middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|137
|left middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|138
|right eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|139
|left eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|140
|skull
|style="background:rgb(241,213,144)"|rgb(241,213,144)
|
|-
|141
|right frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|142
|left frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|143
|right parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|144
|left parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|145
|right temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|146
|left temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|147
|right sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|148
|left sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|149
|right ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|150
|left ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|151
|occipital bone
|style="background:rgb(255,230,138)"|rgb(255,230,138)
|
|-
|152
|maxilla
|style="background:rgb(196,172,68)"|rgb(196,172,68)
|
|-
|153
|right zygomatic bone
|style="background:rgb(255,255,167)"|rgb(255,255,167)
|
|-
|154
|right lacrimal bone
|style="background:rgb(255,250,160)"|rgb(255,250,160)
|
|-
|155
|vomer bone
|style="background:rgb(255,237,145)"|rgb(255,237,145)
|
|-
|156
|right palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|157
|left palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|158
|mandible
|style="background:rgb(222,198,101)"|rgb(222,198,101)
|
|-
|159
|neck
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|160
|muscles of neck
|style="background:rgb(213,124,109)"|rgb(213,124,109)
|
|-
|161
|pharynx
|style="background:rgb(184,105,108)"|rgb(184,105,108)
|
|-
|162
|larynx
|style="background:rgb(150,208,243)"|rgb(150,208,243)
|
|-
|163
|thyroid gland
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|164
|right parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|165
|left parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|166
|skeleton of neck
|style="background:rgb(242,206,142)"|rgb(242,206,142)
|
|-
|167
|hyoid bone
|style="background:rgb(250,210,139)"|rgb(250,210,139)
|
|-
|168
|cervical vertebral column
|style="background:rgb(255,255,207)"|rgb(255,255,207)
|
|-
|169
|thorax
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|170
|trachea
|style="background:rgb(182,228,255)"|rgb(182,228,255)
|
|-
|171
|bronchi
|style="background:rgb(175,216,244)"|rgb(175,216,244)
|
|-
|172
|right lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|173
|left lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|174
|superior lobe of right lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|175
|superior lobe of left lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|176
|middle lobe of right lung
|style="background:rgb(202,164,140)"|rgb(202,164,140)
|
|-
|177
|inferior lobe of right lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|178
|inferior lobe of left lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|179
|pleura
|style="background:rgb(255,245,217)"|rgb(255,245,217)
|
|-
|180
|heart
|style="background:rgb(206,110,84)"|rgb(206,110,84)
|
|-
|181
|right atrium
|style="background:rgb(210,115,89)"|rgb(210,115,89)
|
|-
|182
|left atrium
|style="background:rgb(203,108,81)"|rgb(203,108,81)
|
|-
|183
|atrial septum
|style="background:rgb(233,138,112)"|rgb(233,138,112)
|
|-
|184
|ventricular septum
|style="background:rgb(195,100,73)"|rgb(195,100,73)
|
|-
|185
|right ventricle of heart
|style="background:rgb(181,85,57)"|rgb(181,85,57)
|
|-
|186
|left ventricle of heart
|style="background:rgb(152,55,13)"|rgb(152,55,13)
|
|-
|187
|mitral valve
|style="background:rgb(159,63,27)"|rgb(159,63,27)
|
|-
|188
|tricuspid valve
|style="background:rgb(166,70,38)"|rgb(166,70,38)
|
|-
|189
|aortic valve
|style="background:rgb(218,123,97)"|rgb(218,123,97)
|
|-
|190
|pulmonary valve
|style="background:rgb(225,130,104)"|rgb(225,130,104)
|
|-
|191
|aorta
|style="background:rgb(224,97,76)"|rgb(224,97,76)
|
|-
|192
|pericardium
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|193
|pericardial cavity
|style="background:rgb(184,122,154)"|rgb(184,122,154)
|
|-
|194
|esophagus
|style="background:rgb(211,171,143)"|rgb(211,171,143)
|
|-
|195
|thymus
|style="background:rgb(47,150,103)"|rgb(47,150,103)
|
|-
|196
|mediastinum
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|197
|skin of thoracic wall
|style="background:rgb(173,121,88)"|rgb(173,121,88)
|
|-
|198
|muscles of thoracic wall
|style="background:rgb(188,95,76)"|rgb(188,95,76)
|
|-
|199
|skeleton of thorax
|style="background:rgb(255,239,172)"|rgb(255,239,172)
|
|-
|200
|thoracic vertebral column
|style="background:rgb(226,202,134)"|rgb(226,202,134)
|
|-
|201
|ribs
|style="background:rgb(253,232,158)"|rgb(253,232,158)
|
|-
|202
|sternum
|style="background:rgb(244,217,154)"|rgb(244,217,154)
|
|-
|203
|right clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|204
|left clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|205
|abdominal cavity
|style="background:rgb(186,124,161)"|rgb(186,124,161)
|
|-
|206
|abdomen
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|207
|peritoneum
|style="background:rgb(255,255,220)"|rgb(255,255,220)
|
|-
|208
|omentum
|style="background:rgb(234,234,194)"|rgb(234,234,194)
|
|-
|209
|peritoneal cavity
|style="background:rgb(204,142,178)"|rgb(204,142,178)
|
|-
|210
|retroperitoneal space
|style="background:rgb(180,119,153)"|rgb(180,119,153)
|
|-
|211
|stomach
|style="background:rgb(216,132,105)"|rgb(216,132,105)
|
|-
|212
|duodenum
|style="background:rgb(255,253,229)"|rgb(255,253,229)
|
|-
|213
|small bowel
|style="background:rgb(205,167,142)"|rgb(205,167,142)
|
|-
|214
|colon
|style="background:rgb(204,168,143)"|rgb(204,168,143)
|
|-
|215
|anus
|style="background:rgb(255,224,199)"|rgb(255,224,199)
|
|-
|216
|liver
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|217
|biliary tree
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|218
|gallbladder
|style="background:rgb(139,150,98)"|rgb(139,150,98)
|
|-
|219
|pancreas
|style="background:rgb(249,180,111)"|rgb(249,180,111)
|
|-
|220
|spleen
|style="background:rgb(157,108,162)"|rgb(157,108,162)
|
|-
|221
|urinary system
|style="background:rgb(203,136,116)"|rgb(203,136,116)
|
|-
|222
|right kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|223
|left kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|224
|right ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|225
|left ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|226
|urinary bladder
|style="background:rgb(222,154,132)"|rgb(222,154,132)
|
|-
|227
|urethra
|style="background:rgb(124,186,223)"|rgb(124,186,223)
|
|-
|228
|right adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|229
|left adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|230
|female internal genitalia
|style="background:rgb(244,170,147)"|rgb(244,170,147)
|
|-
|231
|uterus
|style="background:rgb(255,181,158)"|rgb(255,181,158)
|
|-
|232
|right fallopian tube
|style="background:rgb(255,190,165)"|rgb(255,190,165)
|
|-
|233
|left fallopian tube
|style="background:rgb(227,153,130)"|rgb(227,153,130)
|
|-
|234
|right ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|235
|left ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|236
|vagina
|style="background:rgb(193,123,103)"|rgb(193,123,103)
|
|-
|237
|male internal genitalia
|style="background:rgb(216,146,127)"|rgb(216,146,127)
|
|-
|238
|prostate
|style="background:rgb(230,158,140)"|rgb(230,158,140)
|
|-
|239
|right seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|240
|left seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|241
|right deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|242
|left deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|243
|skin of abdominal wall
|style="background:rgb(177,124,92)"|rgb(177,124,92)
|
|-
|244
|muscles of abdominal wall
|style="background:rgb(171,85,68)"|rgb(171,85,68)
|
|-
|245
|skeleton of abdomen
|style="background:rgb(217,198,131)"|rgb(217,198,131)
|
|-
|246
|lumbar vertebral column
|style="background:rgb(212,188,102)"|rgb(212,188,102)
|
|-
|247
|female external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|248
|male external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|249
|skeleton of upper limb
|style="background:rgb(198,175,125)"|rgb(198,175,125)
|
|-
|250
|muscles of upper limb
|style="background:rgb(194,98,79)"|rgb(194,98,79)
|
|-
|251
|right upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|252
|left upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|253
|right shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|254
|left shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|255
|right arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|256
|left arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|257
|right elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|258
|left elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|259
|right forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|260
|left forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|261
|right wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|262
|left wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|263
|right hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|264
|left hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|265
|skeleton of lower limb
|style="background:rgb(255,238,170)"|rgb(255,238,170)
|
|-
|266
|muscles of lower limb
|style="background:rgb(206,111,93)"|rgb(206,111,93)
|
|-
|267
|right lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|268
|left lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|269
|right hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|270
|left hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|271
|right thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|272
|left thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|273
|right knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|274
|left knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|275
|right leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|276
|left leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|277
|right foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|278
|left foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|279
|peripheral nervous system
|style="background:rgb(216,186,0)"|rgb(216,186,0)
|
|-
|280
|autonomic nerve
|style="background:rgb(255,226,77)"|rgb(255,226,77)
|
|-
|281
|sympathetic trunk
|style="background:rgb(255,243,106)"|rgb(255,243,106)
|
|-
|282
|cranial nerves
|style="background:rgb(255,234,92)"|rgb(255,234,92)
|
|-
|283
|vagus nerve
|style="background:rgb(240,210,35)"|rgb(240,210,35)
|
|-
|284
|peripheral nerve
|style="background:rgb(224,194,0)"|rgb(224,194,0)
|
|-
|285
|circulatory system
|style="background:rgb(213,99,79)"|rgb(213,99,79)
|
|-
|286
|systemic arterial system
|style="background:rgb(217,102,81)"|rgb(217,102,81)
|
|-
|287
|systemic venous system
|style="background:rgb(0,147,202)"|rgb(0,147,202)
|
|-
|288
|pulmonary arterial system
|style="background:rgb(0,122,171)"|rgb(0,122,171)
|
|-
|289
|pulmonary venous system
|style="background:rgb(186,77,64)"|rgb(186,77,64)
|
|-
|290
|lymphatic system
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|291
|needle
|style="background:rgb(240,255,30)"|rgb(240,255,30)
|
|-
|292
|region 0
|style="background:rgb(185,232,61)"|rgb(185,232,61)
|
|-
|293
|region 1
|style="background:rgb(0,226,255)"|rgb(0,226,255)
|
|-
|294
|region 2
|style="background:rgb(251,159,255)"|rgb(251,159,255)
|
|-
|295
|region 3
|style="background:rgb(230,169,29)"|rgb(230,169,29)
|
|-
|296
|region 4
|style="background:rgb(0,194,113)"|rgb(0,194,113)
|
|-
|297
|region 5
|style="background:rgb(104,160,249)"|rgb(104,160,249)
|
|-
|298
|region 6
|style="background:rgb(221,108,158)"|rgb(221,108,158)
|
|-
|299
|region 7
|style="background:rgb(137,142,0)"|rgb(137,142,0)
|
|-
|300
|region 8
|style="background:rgb(230,70,0)"|rgb(230,70,0)
|
|-
|301
|region 9
|style="background:rgb(0,147,0)"|rgb(0,147,0)
|
|-
|302
|region 10
|style="background:rgb(0,147,248)"|rgb(0,147,248)
|
|-
|303
|region 11
|style="background:rgb(231,0,206)"|rgb(231,0,206)
|
|-
|304
|region 12
|style="background:rgb(129,78,0)"|rgb(129,78,0)
|
|-
|305
|region 13
|style="background:rgb(0,116,0)"|rgb(0,116,0)
|
|-
|306
|region 14
|style="background:rgb(0,0,255)"|rgb(0,0,255)
|
|-
|307
|region 15
|style="background:rgb(157,0,0)"|rgb(157,0,0)
|
|-
|308
|unknown
|style="background:rgb(100,100,130)"|rgb(100,100,130)
|
|-
|309
|cyst
|style="background:rgb(205,205,100)"|rgb(205,205,100)
|
|-
|}

Documentation/4.1

2012-04-18T19:54:07Z

Demian: /* Diffusion */

__NOTOC__
{{documentation/versionlist}}

=Table of Content=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|

===Slicer Application===
----
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]]

*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts | Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]

*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | '''Computer Configurations''']]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)

*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]

===Mailing Lists===
----
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
:[http://slicer-users.65878.n3.nabble.com/ Search] in archives on nabble.com
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]
:[http://slicer-devel.65872.n3.nabble.com/ Search] in archives on nabble.com



|bgcolor="#CCCCCC"|
|valign="top"|

===Module Categories ===
----
* [[#Core Modules|Core Modules]]
* [[#Wizards|Wizards]]
* [[#Informatics|Informatics]]
* [[#Registration|Registration]]
* [[#Segmentation|Segmentation]]
* [[#Quantification|Quantification]]
* [[#Diffusion|Diffusion]]
* [[#IGT|IGT]]
* [[#Filtering|Filtering]]
* [[#Surface Models|Surface Models]]
* [[#Converters|Converters]]
* [[#Endoscopy|Endoscopy]]
* [[#Developer Tools|Developer Tools]]
* [[#Legacy|Legacy]]
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|valign="top"|

===Miscellaneous===
----


* [[Slicer4:VisualBlog|Visual blog]]
: Set of screenshots showing Slicer in action.


* [[Documentation/4.0/Training|Training pages]]
: Information on how to use Slicer {{documentation/version}}

* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
: Set of common questions/answers

* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]
: Platform specific issues and considerations

* [[Documentation/{{documentation/version}}/Announcements|Announcements]]
: the announcement associated with Slicer {{documentation/version}}

===Developers Corner===
----
* [[Documentation/{{documentation/version}}/Developers | Information for Software Developers]]
: Where to find the source code, how to compile ...
|}

=General Information=
{|width="100%"
|rowspan="3"|
{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer41Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/version}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}
|align="center"|
[[{{collaborator|logo|slicer4}}|x350px]]
|-
|
{{ombox
|type=content
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement]] page for more details. The community contributing to Slicer {{documentation/version}} is acknowledged [http://www.slicer.org/pages/Acknowledgments here].
}}

|}

=Modules by Category=
==Core Modules==
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|GGrayscale Grind Peak Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Endoscopy==
*[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] [[image:UnderConstruction.png|tumb|10px]]

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

=Extensions=
==Introduction==
[[Documentation/4.1/Extensions|Extensions]] which can be added to the basic Slicer package in order to add functionality. The slicer community maintains a website to support finding, downloading and installing Extensions for 3D Slicer 4. Access to this website is integral to Slicer 4 and facilitated by the Extensions Manager functionality built into the distributed program. Please see [[Documentation/{{documentation/version}}/Developers/Tutorials/ExtensionWriting|here]] for information for software developers on how to add your extension to this website.

The download site is referred to as the '''Slicer Extensions Catalog'''. The Catalog classifies extensions into three levels of compliance:
*Category 1: Fully compliant Slicer Extensions: Slicer license, open source, maintained.
*Category 2: open source, contact exists.
*Category 3: all other extensions (work in progress, beta, closed source etc).

See [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionCatalogPolicies|here]] for more information about extension types and policies.

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)[[image:UnderConstruction.png|tumb|10px]]

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]

Documentation/4.1/Modules/TractographyFiducialSeeding

2012-04-18T19:53:26Z

Demian:

Documentation/4.1/Modules/TractographyLabelMapSeeding

2012-04-18T19:53:00Z

Demian:

Documentation/4.1/Modules/DWIToDTIEstimation

2012-04-18T19:50:08Z

Demian:

Slicer4:Diffusion

2012-01-03T19:46:30Z

Demian: /* Goals for the winter NA-MIC week 2012 */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4

[http://na-mic.org/Mantis/search.php?project_id=3&category=Diffusion&sticky_issues=on&sortby=last_updated%2Cstatus&dir=DESC%2CDESC&hide_status_id=90 Mantis Diffusion-related bug list]

-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
'''Suspended Until Jan'''

Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Goals for the winter NA-MIC week 2012=
* Display statistic information for fiber bundles (e.g. FA histogram, mean and dispersion) (Demian Wassermann)
* Integrated interface: Global slicelet with the main diffusion functionalities integrated (Demian Wassermann)
* Peritumoral wizard (Isaiah Norton)
* Ron's proposal for the fiducial seeding interface (combining the functionality of annotations and fiducial seeding)
* Filtered tractography module (Christian Baumgarten, Yogesh Rathi)

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Documentation/4.0/Modules/DWIToDTIEstimation

2011-11-25T23:20:39Z

Demian:

Documentation/4.0/Modules/TractographyDisplay

2011-11-25T23:19:52Z

Demian:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Isaiah Norton, Goldby Lab 
Author: Demian Wassermann, SPL 
Contributor1: Steve Pieper, Isomics Inc. 
Contributor2: Alex YarmarKovich, Isomics Inc. 
Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Allows the user to manipulate several different characteristics of the traced white matter tracts. Examples are: change of color; display of the fractional anisotropy along the tract; display of the tracts as tubes or lines; interactive selection of the tracts; and cropping.






{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
* Use Case 2: Display the tracts as lines or tubes
* Use Case 3: Interactive selection or cropping of a certain bundle.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
*
** Line: Display the tracts as lines
** Tube: Display the tracts as tubes
*** Slice Intersection: Show the tracts in the 2D view
** Glyph: Display glyphs representing the diffusion tensors along the tracts
** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
* Fiber Bundle Selection: Perform interactive selection and cropping of the tracts
** ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts
** Disable/Positive/Negative ROI: Set the selection mode to '''Select everything'''; '''Select the tracts traversing the ROI'''; '''Select the tracts not traversing the ROI'''
** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
* Advance Display: For the lines, tubes and glyphs
** Visibility: Toggle the visibility of the bundle
** Opacity: Change the transparency level of the bundle
** Color By: Change the way the bundle is colored; either by a tensor-derived property or by a group id
** Solid Color: Color the bundle of a single solid color



{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}


{{documentation/{{documentation/version}}/module-footer|category=Example}}

Documentation/4.0/Modules/TractographyDisplay

2011-11-25T23:16:47Z

Demian:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Isaiah Norton, Goldby Lab 
Author: Demian Wassermann, SPL 
Contributor1: Steve Pieper, Isomics Inc. 
Contributor2: Alex YarmarKovich, Isomics Inc. 
Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Allows the user to manipulate several different characteristics of the traced white matter tracts. Examples are: change of color; display of the fractional anisotropy along the tract; display of the tracts as tubes or lines; interactive selection of the tracts; and cropping.






{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
* Use Case 2: Display the tracts as lines or tubes
* Use Case 3: Interactive selection or cropping of a certain bundle.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
*
** Line: Display the tracts as lines
** Tube: Display the tracts as tubes
*** Slice Intersection: Show the tracts in the 2D view
** Glyph: Display glyphs representing the diffusion tensors along the tracts
** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
* Fiber Bundle Selection: Perform interactive selection and cropping of the tracts
** ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts
** Disable/Positive/Negative ROI: Set the selection mode to '''select everything'''; '''select the tracts traversing the ROI'''; '''Select the tracts not traversing the ROI'''
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}


{{documentation/{{documentation/version}}/module-footer|category=Example}}

Documentation/4.0/Modules/TractographyDisplay

2011-11-25T23:11:38Z

Demian:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Isaiah Norton, Goldby Lab 
Author: Demian Wassermann, SPL 
Contributor1: Steve Pieper, Isomics 
Contributor1: Alex Yarmanovich, Isomics 
Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Allows the user to manipulate several different characteristics of the traced white matter tracts. Examples are: change of color; display of the fractional anisotropy along the tract; display of the tracts as tubes or lines; interactive selection of the tracts; and cropping.






{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
* Use Case 2: Display the tracts as lines or tubes
* Use Case 2: Interactive selection or cropping of a certain bundle.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}




{{note}}The section above is generated using the following wiki code:
<pre>
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
</pre>

If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-footer|category=Example}}

Documentation/4.0/Modules/TractographyLabelMapSeeding

2011-11-25T23:02:24Z

Demian:

Documentation/4.0/Modules/TractographyLabelMapSeeding

2011-11-25T23:01:21Z

Demian:

Documentation/4.0/Modules/TractographyDisplay

2011-11-25T21:05:08Z

Demian:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Isaiah Norton, Goldby Lab 
Author: Demian Wassermann, SPL 
Contributor1: Steve Pieper, Isomics 
Contributor1: Alex Yarmanovich, Isomics 
Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.




If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1:
* Use Case 2:


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}




{{note}}The section above is generated using the following wiki code:
<pre>
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
</pre>

If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-footer|category=Example}}

Documentation/4.0/Modules/ResampleDTIVolume

2011-11-18T19:52:41Z

Demian: Created page with ' {{documentation/{{documentation/version}}/module-header}}   {{doc…'

Documentation/4.0

2011-11-18T19:52:25Z

Demian: /* Diffusion */

__NOTOC__
{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/version}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]

{| border="0" align="center" width="70%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|

===Slicer Application===
----
<big>'''
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)

*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)


*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)'''
</big>

===Mailing Lists===
----
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]



|bgcolor="#CCCCCC"|
|valign="top"|

===Module Categories ===
----
<big>'''
* [[#Core Modules|Core Modules]]
* [[#Wizards|Wizards]]
* [[#Informatics|Informatics]]
* [[#Registration|Registration]]
* [[#Segmentation|Segmentation]]
* [[#Quantification|Quantification]]
* [[#Diffusion|Diffusion]]
* [[#IGT|IGT]]
* [[#Filtering|Filtering]]
* [[#Surface Models|Surface Models]]
* [[#Converters|Converters]]
* [[#Endoscopy|Endoscopy]]
* [[#DeveloperTools|Developer Tools]]
* [[#Legacy|Legacy]]
* [[#Utilities|Utility]]
</big>
|bgcolor="#CCCCCC"|
|valign="top"|

===Miscellaneous===
----


* [[Slicer4:VisualBlog|Visual blog]]
: Set of screenshots showing Slicer in action.


* [[Training|Training pages]]
: Information on how to use Slicer {{documentation/version}}

* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
: Set of common questions/answers

===Developers Corner===
----
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]
: Handy Developer Info
|-colspan="3"; align="center"|
<gallery widths=150px heights=150px perrow="4" frameless="yes">
Image:2011-11-12-CroppingWholeBrainTractography-detail.png
Image:Selection 142.png
Image:2011-01-24-Annotation.png
Image:prostate_multiparametric_visualization_Slicer4.png
</gallery>
|}

{{ombox
|type=content
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].
}}

{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}

=Requirements for Modules=
* The module is '''feature complete''', i.e. it does everything that it advertises
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].
*Use the logos in the [[Logo_Gallery|Logo Gallery]]

=Modules by Category=
==Core Modules==
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]

==Wizards==
*Change Tracker (Andrey Fedorov) [[image:UnderConstruction.png|tumb|10px]]

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)

==Segmentation==
*EMSegment Easy (no atlas) (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
**Foreground Masking (BRAINS) (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao) [[image:UnderConstruction.png|tumb|10px]]

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Utilities
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]

==IGT==

==Filtering==
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Resample Tools
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Label Map Smoothing
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*Probe Volume with Model (Paint)

==Converters==
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Endoscopy==
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]]
*Module Template
*Multiple Models Example
*Performance Tests
*Tractography

==Legacy==
*Converters
**BSpline to Deformation Field
*Diffusion
**Denoising
***Unbiased Non Local Means Filter for DWI
*Filtering
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**Resample Scalar Volume
*Registration
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Nonrigid BSpline Registration
**Expert Automated Registration
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Robust Multiresolution Affine Registration
*Segmentation
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

==Utilities==
*Transform MRML Files to NewSegmenter Standard

=Extensions=

'''Introduction'''

* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
* In case of problems with extensions, please talk directly to the developers of the extensions.
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.

==Collections==
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.

{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyCollection
| This is a collection of extensions that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

==Table Of Extensions==
{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something wonderful with your data
| [[File:ExperimentalExtensionIcon.png|80px]]
| [[File:NoSlicerLicenseIcon.png|80px]]
| filter, anisotropic
| my-email at gmail.com
|-
| 2
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

'''Caption for the table of extensions'''
<gallery heights="50px" perrow="4">
Image:SlicerLicenseIcon.png‎| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess) Use with care Might not work all the time Might not be available for all platforms
Image:StableExtensionIcon.png|Stable Full documentation Works as advertised Compiles on all supported platforms Email support works
</gallery>

Documentation/4.0/Modules/DiffusionTensorScalarMeasurements

2011-11-18T19:50:33Z

Documentation/4.0/Modules/TractographyLabelMapSeeding

2011-11-18T19:48:09Z

Documentation/4.0/Modules/DiffusionWeightedVolumeMasking

2011-11-18T19:43:36Z

Demian:

Documentation/4.0/Modules/DWIToDTIEstimation

2011-11-18T19:43:33Z

Demian:

Documentation/4.0/Modules/DWIToDTIEstimation

2011-11-18T19:40:59Z

Demian:

Slicer4:Diffusion

2011-10-25T18:58:12Z

Demian: /* Introduction */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4

[http://na-mic.org/Mantis/search.php?project_id=3&category=Diffusion&sticky_issues=on&sortby=last_updated%2Cstatus&dir=DESC%2CDESC&hide_status_id=90 Mantis Diffusion-related bug list]

-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
'''Suspended Until Jan'''

Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Goals for the winter NA-MIC week 2012=
* Display statistic information for fiber bundles (e.g. FA histogram, mean and dispersion)
* Integrated interface: Global slicelet with the main diffusion functionalities integrated
* Peritumoral wizard
* Ron's proposal for the fiducial seeding interface (combining the functionality of annotations and fiducial seeding)

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-10-25T18:54:23Z

Demian: /* Goals for NA-MIC week 2012 */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
'''Suspended Until Jan'''

Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Goals for the winter NA-MIC week 2012=
* Display statistic information for fiber bundles (e.g. FA histogram, mean and dispersion)
* Integrated interface: Global slicelet with the main diffusion functionalities integrated
* Peritumoral wizard
* Ron's proposal for the fiducial seeding interface (combining the functionality of annotations and fiducial seeding)

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-10-25T18:53:55Z

Demian: /* Introduction */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
'''Suspended Until Jan'''

Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Goals for NA-MIC week 2012=
* Display statistic information for fiber bundles (e.g. FA histogram, mean and dispersion)
* Integrated interface: Global slicelet with the main diffusion functionalities integrated
* Peritumoral wizard
* Ron's proposal for the fiducial seeding interface (combining the functionality of annotations and fiducial seeding)

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-10-25T18:51:11Z

Demian: /* Monthly Slicer4 coding sprint */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
'''Suspended Until Jan'''

Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-10-25T18:51:00Z

Demian: /* Monthly Slicer4 coding sprint */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
'''Suspended Until Jan'''
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-10-25T18:50:34Z

Demian: /* Weekly Meeting */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Bi-Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-10-25T18:50:20Z

Demian: /* Weekly Meeting */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Weekly Meeting ===
Every other Tuesday from 3pm to 4pm teleconference: #800-501-8979 conference code 0235041

=== Monthly Slicer4 coding sprint ===
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-07-05T17:33:22Z

Demian: /* Results after the Summer 2011 NA-MIC meeting */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Weekly Meeting ===
Every Tuesday from 3pm to 4pm at 1249 Boylston, 2nd floor conference room (LMI Suite)

=== Monthly Slicer4 coding sprint ===
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
** Isaiah started porting most of the supporting tools, the same bug as with the other workflows needs to be addressed
* More fluid visualization and exploration of white matter tractographies
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-07-05T17:28:30Z

Demian: /* Features to be addressed before the Summer NA-MIC meeting */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Weekly Meeting ===
Every Tuesday from 3pm to 4pm at 1249 Boylston, 2nd floor conference room (LMI Suite)

=== Monthly Slicer4 coding sprint ===
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Results after the Summer 2011 NA-MIC meeting=
* Porting/profiling of existing functionality
** Working features
*** Importing from DWI
*** Calculating a mask from DWI images
*** Estimating tensors using an arbitrary mask or no mask
*** Fiducial seeding
*** Labelmap seeding
*** Denoising algorithms
*** Import/Export to NIFTI tensor format
*** Finsler tractography and backtracing of the tracts
** Almost working features
*** Visualization of tractography (minor details to be addressed by Alex and Isaiah)
*** Workflows (waiting for bug [[http://www.na-mic.org/Bug/view.php?id=1221 | 1221 ]] to be fixed
** Features to be packed as Slicer 4 extensions
*** Curvature and Dispersion measures (Peter S.)
*** Two tensor tractography (Yogesh)

Features to be addressed in the near future
* Slicer 4 Diffusion Slicelet
* Peritumoral workflow
* More fluid visualization of white matter tracts
* Fluid white matter tract selection and exploration
* Visualization of statistical measures on tracts (mean FA, FA along the tract etc)

Planning diffusion meeting to be scheduled for the week of 25-29th of July

=Features to be addressed before the Summer 2011 NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------

=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-05-25T14:52:16Z

Demian: /* May 2011 */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Weekly Meeting ===
Every Tuesday from 3pm to 4pm at 1249 Boylston, 2nd floor conference room (LMI Suite)

=== Monthly Slicer4 coding sprint ===
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Features to be addressed before the Summer NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------
=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 24
* Issues/bugs to address
** Problems with the shared library/command line mode of some plugins (notably Diffusion Tensor Mathematics)
** Visualization of white matter tracts, mostly done by Isaiah, Alex offered to help.
** Creation of a diffusion tensor supermodule à la Slicer2
** Fix the window/level issues in the color-by-orientation module and the other scalar visualizations of DT data (Julien when he comes back from the other edge of the world)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-05-17T20:31:07Z

Demian: /* May 2011 */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4
-------------------------------
==Periodical Meetings==
=== Weekly Meeting ===
Every Tuesday from 3pm to 4pm at 1249 Boylston, 2nd floor conference room (LMI Suite)

=== Monthly Slicer4 coding sprint ===
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)

Upcoming Tuesdays:
* February 22nd (exceptional 4th Tuesday meeting)
* March 15th
* April 19th
* May 17th

=Features to be addressed before the Summer NA-MIC meeting=
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
-------------------------------
=Schedule until June=

==Jan 2011==
'''Kick-off, First meeting log'''
------------------------------

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
** Labelmap selection module
** Bundle representation
*** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

* Port the fiducial tractography seeding to new infrastructure (Alex)

* Port tensor estimation tools (Demian)

* Implement quick and fluid exploration of pre-calculated full-brain tractographies

* Cluster interactive exploration, cluster labeling (Lauren)

* Fiber laterality module (Lauren)

* Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Feb 2011==
Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.
* Assistants: Steve Pieper, Lauren O'Donnell, Antonio Tristán-Vega, Isaiah Norton and Demian Wassermann
* Main topics addressed:
** CLI interface for diffusion modules on Slicer 4 (and maybe 3): efficient ways of passing the volumes without having to dump them to disk all the time (Isaiah, Steve, Lauren, Demian and some help from Alex)
** Change of concept in slicer 4: from an application with a python interpreter embedded to a python application that can run inside of "any" given python interpreter (Steve, Lauren, Demian)
** Implementation of workflows within the newly developed ctkWorkflow framework (Demian)
** Finsler HARDI tractography (Antonio)

Deliverables Feb: Have detailed plan for March and April (Done!)

==Mar 2011==

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

* Diffusion estimation issues with negative eigenvalues
** It was decided that the DT estimation will output a confidence image
** No correction will be done, if there are too many degenerate tensors, the user will have to use one of our noise/motion correction filters
** The mask generation will be separated from the tensor estimation

Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

==Apr 2011==

Apr 5
* Finsler tractography CLI (Antonio)
** The module is implemented and has appropriate testing
** The modules has been uploaded to NITRC as a project (link)
** Some CMake issues have to be figured out for its proper distribution
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)
** Glyphs are there
** Most DT-based scalars are there
** There seems to be an issue with color by orientation features
* Tractography
** We agreed that Slicer 4 should be able to load vtk files as tractographies and
*** Check that they are only composed of line (no faces)
*** Be able to display tractographies that don't have tensor data greying off the glyphing and coloring options

Apr 12

Apr 19
* Added probe CLI in Slicer3: ProbeVolumeWithModel (Paint)
** Re-checked in this code (Lauren)
** Made it work. Debugged scalar display on models from CLI issue (Lauren, Steve)

Apr 26

Deliverables Apr: Slicer3 CLI for probing,

==May 2011==

May 3

May 10

May17

May 24
*Results of the code sprint
** Fixed colormap window/level (Steve)
** Finished module for Finsler tractography as a NITRC downloadable toolkit including tests (Antonio)
** First implementation of the fiberbundle visualization widget, on a branch for testing (Isaiah)
** Work in progress for the laterality project (Lauren)
** Splitted estimation/masking of the diffusion tensors (Demian)

* Discussion about projects for the summer programming week:
** Nifti Support for Diffusion Tensor Images
** Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
** Refactoring of the tractography display widget (Isaiah)
** Laterality (Lauren)
** Selection for models and bundles post-clustering (Lauren)
** ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
** Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
** Add ODF estimation / visualization (Antonio)

May 31

Deliverable May:

==June 2011==

June: debug, test

June (AHM),

=Reference=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

==File format information==
http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:Community_DTI
* DWI Formats
** http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
** http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
**[[http://www.ncbi.nlm.nih.gov/pubmed/20206274 Proposed Nifti DTI metadata format]]
* Tensor formats
**[[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]]

Slicer4:Diffusion

2011-04-05T20:03:35Z

Demian: /* Apr 2011 */

Slicer4:Diffusion

2011-03-29T19:58:39Z

Demian: /* Monthly Slicer4 coding sprint */

Slicer4:Diffusion

2011-03-29T19:57:47Z

Demian: /* Mar 2011 */

Slicer4:Diffusion

2011-03-29T19:56:17Z

Demian: /* Mar 2011 */

Slicer4:Diffusion

2011-03-08T15:11:36Z

Demian: /* File format information */

Slicer4:Diffusion

2011-02-23T21:04:49Z

Demian: /* Feb 2011 */

Slicer4:VectorImageVisualization

2011-02-21T14:50:14Z

Demian: Created page with 'The main goal of this page is to set the grounds and goals for a common visualization framework for vector images. =Description of vector images= We consider vector-valued image…'

The main goal of this page is to set the grounds and goals for a common visualization framework for vector images.

=Description of vector images=
We consider vector-valued images for the purpose of this project any image composed by several scalar images in which the dimensions and spatial transforms are the same.

Examples of these are:
* DCM-MRI / functional MRI, nowadays handled by Slicer using Junichi's [http://www.na-mic.org/Wiki/index.php/Slicer3:FourDAnalysis | FourDAnalysis module]
* Deformation fields which are the result of a registration process.
* DWI-MRI, currently handled by Slicer.
* DTI-Images could be set under this category but their visualization use-cases are, maybe, far too different from the others.
* More complex representations of diffusion MRI (DSI, Q-Ball, Multishell)

{| border="1" cellpadding="2"
! scope="col" width="50" | Image type
! scope="col" width="225" | 4th axis semantics
! scope="col" width="225" | Number of samples on the 4th axis
|-
| DCM-MRI / fMRI || Time || not fixed
|-
| Deformation field || X,Y,Z components of the transform || 3
|-
| DWI-MRI || a function with domain angle x b-value || not fixed
|-
| DTI-MRI || Components of a symmetric positive definite matrix || 9 (or 6 as there are only 6 independent components)
|-
| More complex representations of diffusion MRI || spherical harmonic coefficients, angular functions, etc || not fixed
|}

=Basic functionalities=

* Multi-component scalar-volume visualization: as with the DWI-images where there is a slider enabling the user to choose which component to visualize
* Glyph-based visualization: maybe this does not make sense for the DCM or other images where the images, but for DWI, Registration, some examples are
** Visualization as vectors (deformation fields, principal diffusion direction)
** Visualization as Ellipsoids or multicuadrics (representation of DT-MRI)
* 2D-plot exploring of a single voxel as in [http://www.na-mic.org/Wiki/index.php/Slicer3:FourDAnalysis | FourDAnalysis module]
* Colormap visualization: Mapping from a 3D vector to the RGB components. Examples are
** DT-MRI visualization
** Direction of the deformation field at each voxel

Slicer4:Diffusion

2011-02-17T16:37:25Z

Demian: /* Schedule until June */

Slicer4:Diffusion

2011-02-17T16:32:34Z

Demian: /* Kick-off, First meeting log */

Slicer4:Diffusion

2011-02-17T16:31:33Z

Demian: /* Kick-off, First meeting log */

Slicer4:Diffusion

2011-02-17T16:30:17Z

Demian:

Slicer4:Diffusion

2011-02-15T21:16:19Z

Demian: /* Features to be addressed */

[[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4

=Jan 2011=
==Outline of plans==

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
* Labelmap selection module
* Bundle representation
** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

Port the fiducial tractography seeding to new infrastructure (Alex)

Port tensor estimation tools (Demian)

Implement quick and fluid exploration of pre-calculated full-brain tractographies

Cluster interactive exploration, cluster labeling (Lauren)

Fiber laterality module (Lauren)

Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Schedule until June==

===Features to be addressed===
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]

* Porting/profiling of existing functionality (Alex)
** '''Getting CLI to a functioning state again (J2/JC)'''
** '''Volumes module including DWI / Tensor'''
** Tensor estimation and scalar extraction
** Tractography seeding (fiducial/labelmap)
** Tensor Visualization (Basic visualization is priority)
** Tractography Visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
* Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
** Python support
*** Multi-threading
*** Weave (without SciPy)
*** Fast LAPACK distribution (now comes with Slicer4)
*** Matplotlib (maybe this will come with PySide)
** CLI Support (Jim Miller?)
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange

Plan to meet weekly on Tuesday afternoons, 1249 Boylston.
-------------------------------
== Proposed Monthly Slicer4 coding sprint: ==

Tuesdays from 12pm to 4pm, third Tuesday of every month, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)
-------------------------------
== Program ==
Feb 1, Discuss overall plan

Feb 8, Define new infrastructure to allow efficient tractography

Feb 15, Define new infrastructure to allow efficient tractography

Feb 22, Discuss user-interface work flow

Deliverables Feb: Have detailed plan for March and April

-------------------------------

Mar 1
* Getting CLI to a functioning state again (Demian is responsible - J2/JC)
* Test the CLIs corresponding to (Isaiah)
** Tensor estimation
** Tensor Scalar extraction
** Tractography seeding (label-map)

Mar 8

Mar 15
* DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

Deliverables Mar: Interactive tractography

-------------------------------

Apr 5
* Finsler tractography CLI (Antonio)
* Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)

Apr 12

Apr 19

Apr 26

Deliverables Apr:

-------------------------------

May 3

May 10

May17

May 24

May 31

Deliverable May:

-------------------------------

June: debug, test

June (AHM),

=Background=
==Workflows==
[http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign#Working_problem:_Slicer3_workflow_for_Tractography:_usability_issues.2C_design_.26_planning JJL & WJP tractography workflow/UI discussion]

[http://www.na-mic.org/publications/item/view/1263 PNL Diffusion MRI Lab Manual]

Slicer4:Diffusion

2011-02-01T19:47:49Z

Demian: /* Jan 2011 */

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4

=Jan 2011=
==Outline of plans==

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

* Single ROI selection module
** Generalization to model hierarchies
* Labelmap selection module
* Bundle representation
** Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

Port the fiducial tractography seeding to new infrastructure (Alex)

Port tensor estimation tools (Demian)

Implement quick and fluid exploration of pre-calculated full-brain tractographies

Cluster interactive exploration, cluster labeling (Lauren)

Fiber laterality module (Lauren)

Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

==Schedule until June==

===Features to be addressed===
* Porting/profiling of existing functionality (Alex)
** Tensor estimation, visualization and scalar extraction
** Tractography (fiducial/labelmap) and visualization
** Displayable manager infrastructure
* Workflows (Demian)
** From DWI to full-brain tractography
** Peritumoral tractography
* DBP/High-end post-processing modules for tractography (Lauren)
** Cluster interaction
** Laterality analysis
** Tumor distance-transform (Isaiah)
* Fluid tractography exploration (Alex, this will be taken care of after the porting/profiling )
** Picking of fibers
** ROI-based selection of fibers
** Labelmap selection of fibers
* Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
* Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )

Plan to meet weekly on Tuesday afternoons, 1249 Boylston.

-------------------------------

Feb 1, Discuss overall plan

Feb 8, Define new infrastructure to allow efficient tractography

Feb 15, Define new infrastructure to allow efficient tractography

Feb 22, Discuss user-interface work flow

Deliverables Feb: Have detailed plan for March and April

-------------------------------

Mar 1

Mar 8

Mar 15

Mar 22

Mar 29

Deliverables Mar: Interactive tractography

-------------------------------

Apr 5

Apr 12

Apr 19

Apr 26

Deliverables Apr:

-------------------------------

May 3

May 10

May17

May 24

May 31

Deliverable May:

-------------------------------

June: debug, test

June (AHM),

Slicer4:Developers

2011-01-26T17:48:24Z

Demian: /* Projects */

''Do not expect to be able to use this page until late 2010 or early 2011 - many things are changing rapidly within the slicer4 code base so just watch the 'public' developer information, until there is a more definitive set of instructions.''

For now, refer to [http://www.na-mic.org/Wiki/images/5/51/2010_Project_Week_Slicer.ppt the 3D Slicer Status Presentation from the June 2010 Project Week] for planning and transition information.

Work on 3D Slicer version 4 has begun in June of 2010. It is expected that Slicer4 will be released in 2011. Please see the [[Slicer4|Slicer4 Description Page]] for detailed information on the current plans.

*For information about older versions of Slicer, see [[Developers|here]].

=Introduction=
*This page of for scientist who write source code, if you want to use a pre-compiled version of Slicer, please go to the [http://www.slicer.org/pages/Special:SlicerDownloads download page].
*Slicer 4 will include a number of fundamental changes to the infrastructure:
**Qt widgets will replace KWW widgets
**CMAKE superbuild will replace getbuildtest

=Compiling=
*how to get the source code
*[[Slicer4:Build_Instructions|how to compile Slicer 4 on your computer]]

=Projects=
(please add your new project to the top of the table)

 
{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Slicer4 Projects'''
|bgcolor="#ddf" valign="top"|'''Key People''' Bold names are responsible for an aspect of the project.
|-
||[[Slicer4:Diffusion|Porting Diffusion from Slicer 3 to 4]]
||'''Demian Wassermann''', Alex Yarmanovich, Steve Pieper
|-
||[[Slicer4:CMAKESuperbuild|CMAKE superbuild]]
||'''Dave Partyka''', Stephen Aylward
|-
||[[Slicer4:Download Data|Download Data Appearance]]
||'''Ron Kikinis''', Julien Jomier
|-
||[[Slicer4:DisplayModule|Slicer 4 Display Module]]
||'''Wendy Plesniak''', Ron Kikinis
|-
||[[Slicer4:VTKWidgets|Slicer 4 VTK Widgets tuning]]
||'''Will Schroeder''', Jean-Christophe Fillion-Robin
|-
||[[Slicer4:UIDesign|Slicer 4 UI design]]
||'''Wendy Plesniak''',
|-
||[[Slicer4:SceneViewsModule|Slicer 4 SceneViews Module]]
||'''Daniel Haehn''',
|-
||[[Slicer4:EMSegment|EM Segmenter]]
||'''Kilian Pohl''', Dominique Belhachemi
|-
||[[Slicer4:Annotation|Annotation]]
||'''Kilian Pohl''', Daniel Haehn
|-
||[[Slicer4:QtPort|Porting Slicer from kww to Qt]]
||'''Julien Finet''', Jean-Christophe Fillion-Robin, Steve Pieper, Stephen Aylward
|}

=Extensions=

 
{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Slicer4 Extensions'''
|bgcolor="#ddf" valign="top"|'''Key People''' Bold names are responsible for an aspect of the project.
|-
||[[Slicer4:VMTK|VMTK]]
||'''Daniel Haehn'''
|-
||[[Slicer4:DTI-EM-Clustering|DTI EM Clustering]]
||'''Mahnaz Maddah''', Jim Miller
|}

= Quick Links for Developers =
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers.

== Slicer 4 Quick links to the Source code ==
The Slicer4 git repository:

*'''Put link here'''

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''General Slicer4 Quick Links'''
|style="background:#ddf" width="40%"|'''Debugging Slicer4 Quick Links'''
|-
||[[Slicer4:Build_Instructions|Slicer4 build instructions]]
||[http://www.cdash.org/CDash/index.php?project=Slicer4 Slicer4 Dashboard (After XX XXXX)]
|-
||Use [http://viewvc.slicer.org ViewVC to browse the repository]
||[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard (Before XX XXXX)]
|-
||[http://www.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for NA-MIC svn]
||[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]
|-
||[http://www.na-mic.org/Slicer/Documentation/Slicer4-doc/html/ Doxygen documentation for Slicer4].
||
|-
||The [[Slicer4:VisualBlog|Slicer4 VisualBlog]] shows screenshots of slicer developments.
||
|-
||Developers should follow the [[Slicer4:Style|Slicer 4 Coding Style]].
|
|}

==Developers' Mailing List ==
Discussion of Slicer 3 and Slicer 4 takes place on the slicer-devel at massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: slicer-devel-request at massmail.spl.harvard.edu with the keyword '''''subscribe''''' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].

Slicer3:3.6 Final Issues

2010-10-13T14:20:33Z

Demian:

==TODO: Issues to fix for the 3.6.2 patch release==
* CompareView issues [http://na-mic.org/Mantis/view.php?id=929 929], [http://na-mic.org/Mantis/view.php?id=936 936] (Jim)
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995]
* VTK GPU Ray Cast flashing (Julien)
** Flickering is mostly fixed !
* Resolve EMSegmenter related issues: (Kilian & friends)
** vtkHTTPHandler is creating broken files [http://na-mic.org/Mantis/view.php?id=955 955] (Wendy)
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Wendy)
* Integrate SPECTRE plugin as an extension (Nicole)
* in the editor module replace the words "Check Points" with the word "Undo" and compress saved label maps into stencils (Steve)
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)
* [http://na-mic.org/Mantis/view.php?id=983 983] FetchMi crashes when deleting entry (Wendy --status: wendy could not reproduce; kilian has provided mrml file that demonstrates problem)
* Katie will create a 32 bit linux version of the modules in the Extension Manager for the release (Katie)
* Failed memory allocation dialog box (Steve) - in slicer3 trunk
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=998 998]
* EMSegmenter segfaults when performing manual sampling

=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing):
**add thumbnails to show effect of the transfer functions,
**remove unneeded ones, correct a typo.
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions.
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)
* Diffusion Tensor Glyphs not showing (Demian)
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
* volume rendering: sampling rate and a few other tweaks (Yanling)
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)

==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==

* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.
* "Change island" effect of Editor is not functioning when the Scope is set to "all"
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]
* EMSegment command line works now with BRAINS (Kilian)
* Removed KWWidgets that do not work under Windows (Kilian)
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)

==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]'''

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)

Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].