2011 Winter Project Week:Breakout Slicer with Ron - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:09:37Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Wjp: /* Preliminary Program */

2011-01-10T21:39:42Z

Preliminary Program

Wjp: /* Preliminary Program */

2011-01-10T21:38:59Z

Preliminary Program

Wjp: /* Preliminary Program */

2011-01-10T21:35:40Z

Preliminary Program

Pieper: /* Preliminary Program */

2011-01-09T15:16:25Z

Preliminary Program

Meier: /* Preliminary Program */

2011-01-09T04:11:30Z

Preliminary Program

Meier: /* Preliminary Program */

2011-01-09T04:10:37Z

Preliminary Program

Meier: /* Preliminary Program */

2011-01-09T03:59:20Z

Preliminary Program

Meier: /* Preliminary Program */

2011-01-09T03:55:54Z

Preliminary Program

Meier: /* Preliminary Program */

2011-01-09T03:54:39Z

Preliminary Program

@@ Line 5: / Line 5: @@
 *This is an advanced topic presentation on Slicer abilities. The intention is to familiarize the NA-MIC community with Slicer abilities.
 *You have mastered the introductions and you are hungry for more.... :)
-**This means that we expect you to at least have worked through the [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training Core Tutorials] before this class.
+**This means that we expect you to at least have worked through the [https://www.slicer.org/wiki/Slicer_3.6:Training Core Tutorials] before this class.
 *Ron and the creators of modules will show you advanced capabilities in Slicer 3.6
 =Logistics=
@@ Line 26: / Line 26: @@
 =Preliminary Program=
 *10 minutes or less per segment
-*Comply with [http://www.slicer.org/slicerWiki/index.php/Documentation-Rons-Rules-For-Tools Rons Rules for Tools]
+*Comply with [https://www.slicer.org/wiki/Documentation-Rons-Rules-For-Tools Rons Rules for Tools]
@@ Line 52: / Line 52: @@
 ***Passing Fiducials to Command Line modules
 ***Fiducial Seeding
-** [http://www.slicer.org/slicerWiki/index.php/Modules:Measurements-Documentation-3.6 Measurements]
+** [https://www.slicer.org/wiki/Modules:Measurements-Documentation-3.6 Measurements]
 ***Ruler (put down two fiducials, Control-m to make a ruler)
 ***Angle
 ***Constraining to slices or models
 *Interactive editor (Steve Pieper)
-** [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor Documentation]
+** [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor Documentation]
-** [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation Description of individual effects]
+** [https://www.slicer.org/wiki/Modules:Editor-Documentation Description of individual effects]
 *Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
 ** [[Media:AHM2011_FastMarching_demo.tgz|Fast Marching demo scene]]
@@ Line 71: / Line 71: @@
 *DTI processing (Alex Yarmarkovich, Demian Wasserman)
 *Volume Cropping (Andrey Fedorov)
-*[http://www.slicer.org/slicerWiki/index.php/Modules:EventBindings-3.6#Slice_Manipulation Keyboard and mouse shortcuts] (Steve Pieper)
+*[https://www.slicer.org/wiki/Modules:EventBindings-3.6#Slice_Manipulation Keyboard and mouse shortcuts] (Steve Pieper)
-*[http://www.slicer.org/slicerWiki/index.php/Modules:VolumeRendering-Documentation-3.6 Volume Rendering] (Yanling Liu/Alex Yarmarkovich/Curtis Lisle)
+*[https://www.slicer.org/wiki/Modules:VolumeRendering-Documentation-3.6 Volume Rendering] (Yanling Liu/Alex Yarmarkovich/Curtis Lisle)
-*[http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmenter-3.6 EM segmentation] (Kilian Pohl)
+*[https://www.slicer.org/wiki/Modules:EMSegmenter-3.6 EM segmentation] (Kilian Pohl)
 =Attendees=

@@ Line 43: / Line 43: @@
 ***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]
 *Compareview (Jim Miller)
-*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) [[http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip fMRICase040.zip]]
+*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) [http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip Sample scene (large) including scene snapshots: fMRICase040.zip]
 *Simple measurements and fiducials (Nicole Aucoin) [http://wiki.na-mic.org/Wiki/index.php/File:FiducialsMeasurementsDemoForAHM2011.zip Sample scene and data with snapshots for fiducials, seeding, measurements]
 ** [[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials tutorial]] and [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Data]

@@ Line 43: / Line 43: @@
 ***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]
 *Compareview (Jim Miller)
-*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) [[/File:FMRI-DTI-SnapshotDemo.zip]]
+*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) [[http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip fMRICase040.zip]]
 *Simple measurements and fiducials (Nicole Aucoin) [http://wiki.na-mic.org/Wiki/index.php/File:FiducialsMeasurementsDemoForAHM2011.zip Sample scene and data with snapshots for fiducials, seeding, measurements]
 ** [[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials tutorial]] and [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Data]

@@ Line 43: / Line 43: @@
 ***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]
 *Compareview (Jim Miller)
-*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich)
+*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) [[/File:FMRI-DTI-SnapshotDemo.zip]]
 *Simple measurements and fiducials (Nicole Aucoin) [http://wiki.na-mic.org/Wiki/index.php/File:FiducialsMeasurementsDemoForAHM2011.zip Sample scene and data with snapshots for fiducials, seeding, measurements]
 ** [[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials tutorial]] and [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Data]

@@ Line 57: / Line 57: @@
 ***Constraining to slices or models
 *Interactive editor (Steve Pieper)
 *Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
 ** [[Media:AHM2011_FastMarching_demo.tgz|Fast Marching demo scene]]

@@ Line 31: / Line 31: @@
 *Registration (Dominik Meier, Hans Johnson)
 **Update: revised dataset and Slicer Scenes for demo here:[[Media:RegDemo_AHM11.zip‎ ]]
-**issues
+**focusing on DTI only: issues
 ***T1 is too high resolution to resample DTI into (will cause memory problems); use subsampled version ''T1_sub'' instead.
 ***initial misalignment is regional only, BSpline portion is sufficient (no affine required)

@@ Line 35: / Line 35: @@
 ***initial misalignment is regional only, BSpline portion is sufficient (no affine required)
 ***masking is required for successful registration: BRAINSfit requires two masks: moving mask for the DTI_base we get from the initial DTI_estimation; for the fixed mask ''T1_sub'' we use the same one but resampled (''T1_sub_mask'').
-***BRAINSfit registration will take ca. 90seconds with default settings and parameters: all defaults except grid size = 7,5,5 ; masking option on
+***BRAINSfit registration will take ca. 90seconds with default settings and parameters as suggested below
-***DTI resampling is done via ''Resample_DTI'' module
+***BRAINSfit parameters: fixed volume: T1_sub, moving volume: DTI_base; check: "include BSpline Registration Phase"; output: ''Slicer BSpline Transform'' : create new; output image volume: create new; output image pixel type: short; Registration parameters: number of grid subsdivisions; = 7,5,5 ;  Control of mask processing: check ''ROI''; input fixed mask = T1_sub_mask; input moving mask: DTI_maskj
-**procedure to register everything to the T1, see here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]
+**DTI resampling is done via ''ResampleDTI Volume'' module. Parameters
 **Resample as needed (DTI, T2 Baseline):
 ***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]