Slicer 4.0:Training - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/images\/([^ ]+) ([^]]+)]" to "[http://www.slicer.org/w/img_auth.php/$1 $2]"

2019-11-27T12:39:16Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/images\/([^ ]+) ([^]]+)]" to "[http://www.slicer.org/w/img_auth.php/$1 $2]"

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:22:04Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Grundlett: Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:18:53Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Nathan.taylor at 16:30, 6 July 2011

2011-07-06T16:30:01Z

Nathan.taylor at 16:22, 6 July 2011

2011-07-06T16:22:47Z

Nathan.taylor at 15:11, 6 July 2011

2011-07-06T15:11:20Z

Nathan.taylor at 15:07, 6 July 2011

2011-07-06T15:07:35Z

Nathan.taylor at 14:53, 6 July 2011

2011-07-06T14:53:55Z

Nathan.taylor at 14:48, 6 July 2011

2011-07-06T14:48:38Z

Nathan.taylor at 21:10, 5 July 2011

2011-07-05T21:10:19Z

@@ Line 18: / Line 18: @@
 | id="Slicer3MinuteTutorial" style="background:#CCFF99; color:blue; font-size:110%" align="center"| '''Core tutorial 1'''
 | style="background:#CCFF99; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf  | Slicer3Minute Tutorial]]'''<br><br><br>1)open slicer. 2)opened data set. 3)rotated model. 4)clicked slice visibility icon (red). 5)turn skin opacity to 0.0. 6) clicked slice visibility icon (green). 7)clip the scull and bone exposing the white matter tissue. 8) move through the scan (green). 9)take visibility off white matter. 10) zoom in and out.
-| style="background:#CCFF99; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/images/5/51/Slicer3MinuteDataset.zip Slicer3Minute Data]'''<br><br> step 2) picture for tutorial is out of date.
+| style="background:#CCFF99; color:black" valign="top" | '''[http://www.slicer.org/w/img_auth.php/5/51/Slicer3MinuteDataset.zip Slicer3Minute Data]'''<br><br> step 2) picture for tutorial is out of date.
 | style="background:#CCFF99; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]
 |-
 | id="Slicer3VisualizationTutorial" style="background:#FFCC99; color:blue; font-size:110%" align="center"| '''Core tutorial 2'''
 | style="background:#FFCC99; color:black" valign="top"| '''[[media:Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf‎‎ ‎ | Slicer3Visualization Tutorial]]'''<br><br><br>1) open slicer. 2) parts of slicer. 3) load volume 001.dcm from dicom directory. 4) open module volumes. 5) using window/level slider. 6) open volume spgr.nhdr. 7) select red only layout from the choose view icon. 8) fit the image size to window. 9) click foreground icon and select the dicom image. 10)change display using the background/foreground icons. 11)use slider to display ventricles. 12) go back to standard view. PART 2 1) select volume file.<br><br>
-| style="background:#FFCC99; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Slicer3Visualization Data]'''<br><br>step 2)edit tutorial no progress bar. step 3)a)slicer does not display the dicom header information, b) new tutorial image is needed c)click open not apply. step 5) new tutorial image is needed. step 11)scans improperly under (-30) (red) unsure if it is slicer or the selected data set. PART 2 step 1)the loading menu is missing, unable to do any more on this tutorial without it.
+| style="background:#FFCC99; color:black" valign="top" | '''[http://www.slicer.org/w/img_auth.php/6/61/Slicer3VisualizationDataset.zip Slicer3Visualization Data]'''<br><br>step 2)edit tutorial no progress bar. step 3)a)slicer does not display the dicom header information, b) new tutorial image is needed c)click open not apply. step 5) new tutorial image is needed. step 11)scans improperly under (-30) (red) unsure if it is slicer or the selected data set. PART 2 step 1)the loading menu is missing, unable to do any more on this tutorial without it.
 | style="background:#FFCC99; color:black" align="center"| [[Image:VisualizationTutorial 3.6RC3.png|250px]]
 |-
@@ Line 43: / Line 43: @@
 | id="ManualRegistration" style="background:#FFCC33; color:blue; font-size:110%" align="center"|  '''Core tutorial 6'''
 | style="background:#FFCC33; color:black" valign="top"|'''[[media:ManualRegistration_Slicer3.6.pdf‎  | Manual Registration]] ''' <br><br><br> 1) open slicer. 2)upload "ManualRegistrationExample_SlicerScene.mrml". 3)select 4-up. 4) link views. 5) set foreground to moving. 6)set background to fixed. 7)set the visibility slider to halfway between the two. 8) open data module. 9) select the new node. 10)rename it Manuallnit. 11) drag MRI_Moving on top of Manuallnit. 12) open the transforms module. 13) Move slider "IS" to (-21). 14) move slider "PA" to (-24). 15) move slider "IS" to 14. 16) move slider "LR" to 26. 17)save file! <br><br>'''Audience:''' First time & early users.
-| style="background:#FFCC33; color:black" valign="top"|'''[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]'''<br><br>step 10) tutorial says to enter it in a name field but on Slicer4 you need to double-click it. step 13) you must first select transform node: manuallnit.
+| style="background:#FFCC33; color:black" valign="top"|'''[http://www.slicer.org/w/img_auth.php/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]'''<br><br>step 10) tutorial says to enter it in a name field but on Slicer4 you need to double-click it. step 13) you must first select transform node: manuallnit.
 | style="background:#FFCC33; color:black" align="center"|[[Image:Slicer3_ManualRegistrationTutorial.gif|250px]]
 |-
 | id="DiffusionMRITutorial" style="background:#FFCC99; color:blue; font-size:110%" align="center"| '''Specialized tutorial 1'''
 | style="background:#FFCC99; color:black" valign="top"|'''[[Media:DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf‎ | Diffusion MRI tutorial]]''' <br><br><br>1) open slicer. 2) upload dwiDataset.nhdr. 3) open Volumes module. 4) set dwiDataset as Active Volume. 5) open the Diffusion Tensor Estimation module. 6) plug in the dwiDataset as the Input DWI Volume. 7) set output to create new DiffusionTensorVolume. 8) set Otsu Threshold Mask to Create New Volume. 9) select tensor Estimation Algorithm LS. 10) click apply.  <br><br>'''Audience:''' All users and developers.
-| style="background:#FFCC99; color:black" valign="top" |'''[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]''' step 8)there is no setting called Otsu Threshold Mask, i tried twice once replacing Otsu Mask with output baseline volume, because Diffusion Tensor Mask has no Create New Volume setting. 10) project can go no further due to errors in step 8.
+| style="background:#FFCC99; color:black" valign="top" |'''[http://www.slicer.org/w/img_auth.php/c/cf/DiffusionDataset.zip Diffusion Data]''' step 8)there is no setting called Otsu Threshold Mask, i tried twice once replacing Otsu Mask with output baseline volume, because Diffusion Tensor Mask has no Create New Volume setting. 10) project can go no further due to errors in step 8.
 | style="background:#FFCC99; color:black" align="center"|[[Image:cc.PNG |250px]]
 |-
@@ Line 74: / Line 74: @@
 | id="EMSegmenterSimpleMode" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''
 | style="background:#FFFFCC; color:black"  valign="top"| [[media:EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf | '''EMSegmenter Simple Mode ''']] <br><br> This tutorial takes the trainee through the segmentation of a MRI Human Brain without to adjust any parameters.
-| style="background:#FFFFCC; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/c/cd/MRIHumanBrain_T1_aligned.nrrd '''Human Brain T1 Data''']
+| style="background:#FFFFCC; color:black" valign="top" | [http://www.slicer.org/w/img_auth.php/c/cd/MRIHumanBrain_T1_aligned.nrrd '''Human Brain T1 Data''']
 | style="background:#FFFFCC; color:black" align="center"| [[Image:EMSegmenter-Simple-Mode.png|250px]]
 |-
 | id="EMSegmenterAdvancedMode" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''
 | style="background:#FFFFCC; color:black"  valign="top"| [[media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf | '''EMSegmenter Advanced Mode ''']] <br><br> This tutorial takes the trainee through the segmentation of a MRI Human Brain. The trainee will learn how to setup the EMSegmenter, this includes the creation of a task, the creation of an anatomical tree and adjusting the weights for the EM algorithm.
-| style="background:#FFFFCC; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/c/cd/MRIHumanBrain_T1_aligned.nrrd '''Human Brain T1 Data''']
+| style="background:#FFFFCC; color:black" valign="top" | [http://www.slicer.org/w/img_auth.php/c/cd/MRIHumanBrain_T1_aligned.nrrd '''Human Brain T1 Data''']
 | style="background:#FFFFCC; color:black" align="center"| [[Image:EMSegmenter-Advanced-Mode.png|250px]]
 |-

@@ Line 38: / Line 38: @@
 | id="InteractiveEditor" style="background:#FFCC99; color:blue; font-size:110%" align="center"|  '''Core tutorial 5'''
 | style="background:#FFCC99; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf |Interactive Editor]] '''<br><br><br>1) open slicer. 2) upload "grayscale.nrrd". 3) open editor module. 4) set master volume to grayscale. 5) select "GenericAtonomyColors" Color map and apply it. <br>'''Audience:''' All users and developers.
-| style="background:#FFCC99; color:black" valign="top"|'''[http://www.slicer.org/slicerWiki/index.php/File:EditorTutorialDataset.zip Editor Data]'''<br><br>step 5) the editor does not display the frame that contains different tools for editing.
+| style="background:#FFCC99; color:black" valign="top"|'''[[File:EditorTutorialDataset.zip|Editor Data]]'''<br><br>step 5) the editor does not display the frame that contains different tools for editing.
 | style="background:#FFCC99; color:black" align="center"|[[Image:InteractiveEditor.png|250px]]
 |-

@@ Line 84: / Line 84: @@
 | id="OpenIGTLink" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''
 | style="background:#FFFFCC; color:black"  valign="top"|[[media:OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.pdf‎ | '''OpenIGTLink''']] <br><br> This tutorial shows to connect an IGT device using the OpenIGTLink.
-|style="background:#FFFFCC; color:black" valign="top" | [http://wiki.slicer.org/slicerWiki/index.php/Modules:OpenIGTLinkIF-3.6-Simulators'''OpenIGTLink Data Simulator''']
+|style="background:#FFFFCC; color:black" valign="top" | [[Modules:OpenIGTLinkIF-3.6-Simulators'''OpenIGTLink|Data Simulator''']]
 | style="background:#FFFFCC; color:black" align="center"| [[Image:OpenIGT.PNG|250px]]
 |-

@@ Line 56: / Line 56: @@
 | style="background:#FFCC99; color:black" align="center"|[[Image:Slicer3.4.1-ChangeTracker.jpg|250px]]
 |-
-| id="FreeSurferCourse" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized tutorial 3'''
+| id="FreeSurferCourse" style="background:#FFCC99; color:blue; font-size:110%" align="center"|  '''Specialized tutorial 3'''
-| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ |  FreeSurfer Course ]]''' 1) open slicer. 2) go to Volumes module. 3) click on select volume file. 4) open brain.mgz centered. 5)link the slices and make them visible. 6) repeat step 3. 7) click label map and apply. 8) click look up table than FreeSurferLables. 9)look through labels. <br> PART 2 <br> 1) select model maker from modules. 2) make input volume aseg. 3) select models make a new hierarchy. 4)name the model right-hippocampus and uncheck generate all models. 5)under parameters enter #53 as a label. 6)turn off slice visibility. 7) apply.
+| style="background:#FFCC99; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ |  FreeSurfer Course ]]'''<br><br> 1) open slicer. 2) go to Volumes module. 3) click on select volume file. 4) open brain.mgz centered. 5)link the slices and make them visible. 6) repeat step 3. 7) click label map and apply. 8) click look up table than FreeSurferLables. 9)look through labels. <br> PART 2 <br> 1) select model maker from modules. 2) make input volume aseg. 3) select models make a new hierarchy. 4)name the model right-hippocampus and uncheck generate all models. 5)under parameters enter #53 as a label. 6)turn off slice visibility. 7) apply.
 <br><br>'''Audience:''' All users
-| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip  FreeSurfer tutorial data ''']
+| style="background:#FFCC99; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip  FreeSurfer tutorial data ''']<br><br> step 3)does not exist instead i went through the file menu. step 6) same problem as step 3, same solution. step 7) instead click volume information then click label map. <br>PART 2<br>step 7) "completed with errors" no image is displayed.
-| style="background:#FFFFCC; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
+| style="background:#FFCC99; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
 |-
 | id="NeurosurgicalPlanningTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''

@@ Line 56: / Line 56: @@
 | style="background:#FFCC99; color:black" align="center"|[[Image:Slicer3.4.1-ChangeTracker.jpg|250px]]
 |-
-| id="FreeSurferCourse" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''
+| id="FreeSurferCourse" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized tutorial 3'''
-| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ |  FreeSurfer Course ]]''' The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
+| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ |  FreeSurfer Course ]]''' 1) open slicer. 2) go to Volumes module. 3) click on select volume file. 4) open brain.mgz centered. 5)link the slices and make them visible. 6) repeat step 3. 7) click label map and apply. 8) click look up table than FreeSurferLables. 9)look through labels. <br> PART 2 <br> 1) select model maker from modules. 2) make input volume aseg. 3) select models make a new hierarchy. 4)name the model right-hippocampus and uncheck generate all models. 5)under parameters enter #53 as a label. 6)turn off slice visibility. 7) apply.
 <br><br>'''Audience:''' All users
 | style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip  FreeSurfer tutorial data ''']

@@ Line 51: / Line 51: @@
 | style="background:#FFCC99; color:black" align="center"|[[Image:cc.PNG |250px]]
 |-
-| id="ChangeTrackerTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized tutorial 2'''
+| id="ChangeTrackerTutorial" style="background:#FFCC99; color:blue; font-size:110%" align="center"|  '''Specialized tutorial 2'''
-| style="background:#FFFFCC; color:black" valign="top"|'''[[media:Slicer3.6-ChangeTrackerTutorial.pdf‎ |  Change Tracker Tutorial]]''' <br><br><br>1)open slicer 2) go to modules then Wizards then Change Tracker <br><br>'''Audience:''' All users interested in longitudinal analysis of pathology.
+| style="background:#FFCC99; color:black" valign="top"|'''[[media:Slicer3.6-ChangeTrackerTutorial.pdf‎ |  Change Tracker Tutorial]]''' <br><br><br>1)open slicer 2) go to modules then Wizards then Change Tracker <br><br>'''Audience:''' All users interested in longitudinal analysis of pathology.
-| style="background:#FFFFCC; color:black" valign="top" |step 2) the Wizards menu option does not expand, nor does IGT, but all the others work fine.
+| style="background:#FFCC99; color:black" valign="top" |step 2) the Wizards menu option does not expand, nor does IGT, but all the others work fine.
-| style="background:#FFFFCC; color:black" align="center"|[[Image:Slicer3.4.1-ChangeTracker.jpg|250px]]
+| style="background:#FFCC99; color:black" align="center"|[[Image:Slicer3.4.1-ChangeTracker.jpg|250px]]
 |-
 | id="FreeSurferCourse" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''

@@ Line 46: / Line 46: @@
 | style="background:#FFCC33; color:black" align="center"|[[Image:Slicer3_ManualRegistrationTutorial.gif|250px]]
 |-
-| id="DiffusionMRITutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
+| id="DiffusionMRITutorial" style="background:#FFCC99; color:blue; font-size:110%" align="center"| '''Specialized tutorial 1'''
-| style="background:#FFFFCC; color:black" valign="top"|'''[[Media:DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf‎ | Diffusion MRI tutorial]]''' <br><br><br>This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. <br><br>'''Audience:''' All users and developers.
+| style="background:#FFCC99; color:black" valign="top"|'''[[Media:DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf‎ | Diffusion MRI tutorial]]''' <br><br><br>1) open slicer. 2) upload dwiDataset.nhdr. 3) open Volumes module. 4) set dwiDataset as Active Volume. 5) open the Diffusion Tensor Estimation module. 6) plug in the dwiDataset as the Input DWI Volume. 7) set output to create new DiffusionTensorVolume. 8) set Otsu Threshold Mask to Create New Volume. 9) select tensor Estimation Algorithm LS. 10) click apply.  <br><br>'''Audience:''' All users and developers.
-| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]'''
+| style="background:#FFCC99; color:black" valign="top" |'''[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]'''
-| style="background:#FFFFCC; color:black" align="center"|[[Image:cc.PNG |250px]]
+| style="background:#FFCC99; color:black" align="center"|[[Image:cc.PNG |250px]]
 |-
 | id="ChangeTrackerTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"|  '''Specialized'''