Modules:StochasticTractography-Documentation-3.4 - Revision history

Reckbo at 21:14, 30 March 2010

2010-03-30T21:14:42Z

Marianna at 20:32, 26 May 2009

2009-05-26T20:32:06Z

Marianna at 20:08, 26 May 2009

2009-05-26T20:08:38Z

Jvs at 18:52, 16 April 2009

2009-04-16T18:52:44Z

Jvs at 18:50, 16 April 2009

2009-04-16T18:50:00Z

Jvs at 16:20, 16 April 2009

2009-04-16T16:20:17Z

Jvs at 01:18, 16 April 2009

2009-04-16T01:18:28Z

Jvs at 01:15, 16 April 2009

2009-04-16T01:15:33Z

Jvs at 01:13, 16 April 2009

2009-04-16T01:13:59Z

Jvs at 01:10, 16 April 2009

2009-04-16T01:10:40Z

@@ Line 21: / Line 21: @@
 * Author: Julien von Siebenthal
 * Contributor: Steve Pieper
-* Contact: jvs at bwh.harvard.edu
+* Contact: Ryan Eckbo, PNL, reckbo at bwh.harvard.edu
 ===Module Description===

@@ Line 21: / Line 21: @@
 * Author: Julien von Siebenthal
 * Contributor: Steve Pieper
-* Contact: jvs@bwh.harvard.edu
+* Contact: jvs at bwh.harvard.edu
 ===Module Description===

@@ Line 1: / Line 1: @@
- [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
+[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===

@@ Line 101: / Line 101: @@
 ** Input ROI Volume (A/B): only 1 ROI is needed to achieve a tractography. If you want to evaluate the connection between two regions, you will give both ROIs
 ** Input WM Volume: a white matter mask can be given as input to use ones provided by other tools or Slicer modules - it will supersede the brain mask even if enabled. Be mindful in setting a WM: tractography results can be impaired by a too restrictive WM
-** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 steps just require a DWI
+** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 features just require a DWI
 {|
 |[[Image:IOmenu.png|thumb|500px|IO step]]

@@ Line 23: / Line 23: @@
 ===Module Description===
 As a main purpose, the stochastic tractography module helps to evaluate connectivity between two regions of interest (ROIs) of the brain. These ROIs define generally grey matter regions having a specific neurophysiological function. Extensively, study involving more than two regions could still be done by pairing the regions two by two.
 == Usage ==
@@ Line 90: / Line 92: @@
 |}
-* [http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial link tutorial]
 ===Quick Tour of Features and Use===

@@ Line 160: / Line 160: @@
 *** mThird: tracts only counted have length between (maximum tract length)/3 and 2 * (maximum tract length)/3
 *** uThird: tracts only counted have length between 2 * (maximum tract length)/3 and (maximum tract length)
 {|
 |[[Image:Connectmenu.png|thumb|500px|Connectivity step]]

@@ Line 96: / Line 96: @@
+|
 * '''IO panel:'''
-** Input DWI Volume: the DWI is loaded through the Volume module - it is th only mandatory input.
+** Input DWI Volume: the DWI is loaded through the Volume module - it is th only mandatory input
-** Input ROI Volume (A/B): only 1 ROI is needed to achieve a tractography. If you want to evaluate the connection between two regions, you will give both ROIs.
+** Input ROI Volume (A/B): only 1 ROI is needed to achieve a tractography. If you want to evaluate the connection between two regions, you will give both ROIs
-** Input WM Volume: a white matter mask can be given as input to use ones provided by other tools or Slicer modules - it will supersede the brain mask even if enabled. Be mindful in setting a WM: tractography results can be impaired by a too restrictive WM.
+** Input WM Volume: a white matter mask can be given as input to use ones provided by other tools or Slicer modules - it will supersede the brain mask even if enabled. Be mindful in setting a WM: tractography results can be impaired by a too restrictive WM
-** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 steps just require a DWI.
+** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 steps just require a DWI
 {|
 |[[Image:IOmenu.png|thumb|500px|IO step]]
@@ Line 108: / Line 108: @@
+|
 * '''Smoothing panel:'''
-** Gaussian FWHM: this filter defines a Full Width Half Maximum. You can define it for each direction in modifying each component of the 3-vector.
+** Gaussian FWHM: this filter defines a Full Width Half Maximum. You can define it for each direction in modifying each component of the 3-vector
-** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction.
+** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
 {|
 |[[Image:Smoothmenu.png|thumb|500px|Smoothing step]]
@@ Line 118: / Line 118: @@
+|
 * '''Brain Mask panel:'''
-** Lower/Higher Brain Threshold: this filter is based on a simple level set segmentation - intensities of the baseline lying between the two values will be represented, others are set to 0. The most common use of this filter is to remove ventricles from the tractography domain and most of the outside of the brain.
+** Lower/Higher Brain Threshold: this filter is based on a simple level set segmentation - intensities of the baseline lying between the two values will be represented, others are set to 0. The most common use of this filter is to remove ventricles from the tractography domain and most of the outside of the brain
-** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction.
+** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
 {|
 |[[Image:Maskmenu.png|thumb|500px|Brain mask step]]
@@ Line 128: / Line 128: @@
+|
 * '''Diffusion Tensor panel:'''
-** Important: this step is not mandatory. It is here to evaluate the whole tensor and achieve measurements like FA, mode or trace. You did not need it to achieve tractography.
+** Important: this step is not mandatory. It is here to evaluate the whole tensor and achieve measurements like FA, mode or trace. You did not need it to achieve tractography
-** FA, mode and trace are sent as scalar volumes and inserted in the MRML tree to be further used.
+** FA, mode and trace are sent as scalar volumes and inserted in the MRML tree to be further used
-** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction.
+** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
 {|
 |[[Image:Tensormenu.png|thumb|500px|Tensor step]]
@@ Line 139: / Line 139: @@
+|
 * '''Tractography panel:''' This panel deals with the tractography per se:
-** Total tracts: number of generated tracts per voxel.
+** Total tracts: number of generated tracts per voxel
-** Maximum tract length (mm): set the maximum length a tract could reach.
+** Maximum tract length (mm): set the maximum length a tract could reach
-** Step size (mm): is the step length for the update vector.
+** Step size (mm): is the step length for the update vector
-** Use spacing: must be used with caution - activate spacing of the update vector.
+** Use spacing: must be used with caution - activate spacing of the update vector
-** Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use it in most cases.
+** Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use it in most cases
 {|
 |[[Image:Tractomenu.png|thumb|500px|Tractography step]]

@@ Line 38: / Line 38: @@
+|
 * Feature 1 : smooth the given Diffusion Weighted Image (DWI) using a Half Width Full Maximum gaussian filter
-[[Image:smooth2.png|thumb|500px|Smoothing step]]
+{|
 |}
@@ Line 44: / Line 46: @@
+|
 * Feature 2 : generate a brain mask from the DWI baseline input
-[[Image:mask2.png|thumb|500px|Brain mask step]]
+{|
 |}

@@ Line 37: / Line 37: @@
 {|
+|
-* Feature 1 : smooth using a Half Width Full Maximum gaussian filter
+* Feature 1 : smooth the given Diffusion Weighted Image (DWI) using a Half Width Full Maximum gaussian filter
 [[Image:smooth2.png|thumb|500px|Smoothing step]]
 |}
@@ Line 43: / Line 43: @@
 {|
+|
-* Feature 2 : generate a brain mask
+* Feature 2 : generate a brain mask from the DWI baseline input
 [[Image:mask2.png|thumb|500px|Brain mask step]]
 |}
@@ Line 49: / Line 49: @@
 {|
+|
-* Feature 3 : create a DTI (Diffusion Tensor Image) tensor
+* Feature 3 : create a DTI (Diffusion Tensor Image) tensor from the DWI input
 {|
 |[[Image:tensor2.png|thumb|500px|Tensor step]]
@@ Line 67: / Line 67: @@
 {|
+|
-* Feature 5 : produce connection maps in case 2 ROIs are given without ROI filtering
+* Feature 5 : produce connection maps in case 2 ROIs are given without ROI filtering from the tractography
 ** showing union and intersection of both maps from region A to region B and B to A
 {|
@@ Line 77: / Line 77: @@
 {|
+|
-* Feature 6 : produce connection maps in case 2 ROIs are given with ROI filtering
+* Feature 6 : produce connection maps in case 2 ROIs are given with ROI filtering from the tractography
 ** showing only tracts connecting region A to region B and B to A
 {|

@@ Line 147: / Line 147: @@
 {|
+|
-* '''Connectivity Map panel:''' This panel lets the user modify parameters to create density/connectivity maps. A map is a scalar volume storing the number of times each voxel is traversed by tracts. It can be counted differently which the purpose of the following parameters:
+* '''Connectivity Map panel:''' This panel lets the user modify parameters to create density/connectivity maps. A map is a scalar volume storing the number of times each voxel is traversed by tracts. It can be counted differently which is the purpose of the following parameters:
 ** Computation mode:
 *** binary: voxel counter is incremented by 1 only once