Difference between revisions of "2011 Winter Project Week:Breakout Slicer with Ron"

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*This is an advanced topic presentation on Slicer abilities. The intention is to familiarize the NA-MIC community with Slicer abilities.
 
*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.... :)
 
*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
 
*Ron and the creators of modules will show you advanced capabilities in Slicer 3.6
 
=Logistics=
 
=Logistics=
 
*What: Advanced capabilities in Slicer
 
*What: Advanced capabilities in Slicer
 
*Who: All the new DBP engineers, all the participants new to NA-MIC
 
*Who: All the new DBP engineers, all the participants new to NA-MIC
−
*When: Wednesday afternoon: 1pm through 3pm
+
*When: Monday afternoon: 3pm through 5pm
−
*Where: Room XXXX
+
*Where: Main Event Room
  
 
=Data=
 
=Data=
Line 21: Line 21:
 
image:Case40-SPGRwGD.png|SPGR after injection of Gd
 
image:Case40-SPGRwGD.png|SPGR after injection of Gd
 
image:Case40-DTI.png|DTI color by orientation overlayed over T2 baseline
 
image:Case40-DTI.png|DTI color by orientation overlayed over T2 baseline
 +
image:Case40Annotation.png|Annotation of some of the structures
 
</gallery>
 
</gallery>
  
 
=Preliminary Program=
 
=Preliminary Program=
 
*10 minutes or less per segment
 
*10 minutes or less per segment
−
*Registration (Dominik Meier)
+
*Comply with [https://www.slicer.org/wiki/Documentation-Rons-Rules-For-Tools Rons Rules for Tools]
 +
 
 +
 
 +
*Registration (Dominik Meier, Hans Johnson)
 +
**Update: revised dataset and Slicer Scenes for demo here:[[Media:RegDemo_AHM11.zip‎ ]]
 +
**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)
 +
***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 as suggested below
 +
***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
 +
**DTI resampling is done via ''ResampleDTI Volume'' module. Parameters
 +
*** Input Volume: DTI, Output Volume: create new; Reference Volume: "T2-sub";  Transform Node: Bspline Xform produced by BRAINSfit, check ''output-to-input" box.
 +
**for the procedures to register '''everything''' to the T1 (incl. contrast, FLAIR, T2) , see here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]
 +
**Resample as needed (DTI, T2 Baseline):
 +
***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']]
 
*Compareview (Jim Miller)
 
*Compareview (Jim Miller)
−
*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovic)
+
*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)
+
*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]
 +
***Adding and Deleting Fiducials
 +
***Editing Fiducials
 +
***Display properties
 +
***Linking (control key+mouse move) and jumping slices (right click in table)
 +
***Passing Fiducials to Command Line modules
 +
***Fiducial Seeding
 +
** [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)
 
*Interactive editor (Steve Pieper)
 +
** [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor Documentation]
 +
** [https://www.slicer.org/wiki/Modules:Editor-Documentation Description of individual effects]
 
*Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
 
*Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
−
*DTI processing (Alex Yarmarkovic, Demian Wasserman)
+
** [[Media:AHM2011_FastMarching_demo.tgz|Fast Marching demo scene]]
 +
*** inner part of the tumor segmented from SPGR
 +
*** outer part of the tumor segmented from post-Gad
 +
*** WM and GM segmented from N4-processed SPGR (WM segmentation of the original SPGR volume is included, note under-segmented WM in the skull base)
 +
*** all segmentations were done using FastMarching, fiducials are included for each of the segmentations
 +
*** no fine-tuning of the fiducial locations was done -- this is an example result one can get almost right away
 +
*** rule of thumb in placing fiducials: try to cover uniformly the volume you are trying to segment; this is particularly important for large structures like WM/GM
 +
** [[Media:AHM2011_RSS_demo.zip|RSS demo scene]]
 +
*** Segment the inner part of the tumor from SPGR using RSS
 +
*DTI processing (Alex Yarmarkovich, Demian Wasserman)
 
*Volume Cropping (Andrey Fedorov)
 
*Volume Cropping (Andrey Fedorov)
−
*Keyboard and mouse shortcuts (Steve Pieper)
+
*[https://www.slicer.org/wiki/Modules:EventBindings-3.6#Slice_Manipulation Keyboard and mouse shortcuts] (Steve Pieper)
−
*Volume Rendering (Yanling Liu/Alex Yarmarkovic)
+
*[https://www.slicer.org/wiki/Modules:VolumeRendering-Documentation-3.6 Volume Rendering] (Yanling Liu/Alex Yarmarkovich/Curtis Lisle)
−
*EM segmentation (Kilian Pohl, Marcel Prastawa)
+
*[https://www.slicer.org/wiki/Modules:EMSegmenter-3.6 EM segmentation] (Kilian Pohl)
  
 
=Attendees=
 
=Attendees=
 
#Ron Kikinis
 
#Ron Kikinis
 
#Steve Pieper
 
#Steve Pieper
 +
#UCLA DBP Engineer: Andrei Irimia
 +
#Iowa DBP Engineer: Mark Scully
 +
#MGH DBP Engineer: Nadya Shusharina
 +
#Utah DBP Engineer: Josh Cates
 +
#Utah DBP Student: Josh Blauer
 +
#Utah DBP PI: Rob MacLeod
 +
#Utah DBP Student: Chris Gloschat

Latest revision as of 17:09, 10 July 2017

Home < 2011 Winter Project Week:Breakout Slicer with Ron
 Back to  Project Week Agenda

Moderator: Ron Kikinis

Introduction

  • 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 Core Tutorials before this class.
  • Ron and the creators of modules will show you advanced capabilities in Slicer 3.6

Logistics

  • What: Advanced capabilities in Slicer
  • Who: All the new DBP engineers, all the participants new to NA-MIC
  • When: Monday afternoon: 3pm through 5pm
  • Where: Main Event Room

Data

  • Image data used

  • Case 40 from the fMRI neurosurgery data set on central.xnat.org

  • T1 Weighted SPGR image

  • T2 weighted Bzero image derived from the DWI acquisition

  • FLAIR image

  • SPGR after injection of Gd

  • DTI color by orientation overlayed over T2 baseline

  • Annotation of some of the structures

Preliminary Program


  • Registration (Dominik Meier, Hans Johnson)
    • Update: revised dataset and Slicer Scenes for demo here:Media:RegDemo_AHM11.zip‎
    • 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)
      • 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 as suggested below
      • 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
    • DTI resampling is done via ResampleDTI Volume module. Parameters
      • Input Volume: DTI, Output Volume: create new; Reference Volume: "T2-sub"; Transform Node: Bspline Xform produced by BRAINSfit, check output-to-input" box.
    • for the procedures to register everything to the T1 (incl. contrast, FLAIR, T2) , see here: Reg.Lib Case 33
    • Resample as needed (DTI, T2 Baseline):
  • Compareview (Jim Miller)
  • Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) Sample scene (large) including scene snapshots: fMRICase040.zip
  • Simple measurements and fiducials (Nicole Aucoin) Sample scene and data with snapshots for fiducials, seeding, measurements
    • Fiducials tutorial and Data
      • Adding and Deleting Fiducials
      • Editing Fiducials
      • Display properties
      • Linking (control key+mouse move) and jumping slices (right click in table)
      • Passing Fiducials to Command Line modules
      • Fiducial Seeding
    • Measurements
      • Ruler (put down two fiducials, Control-m to make a ruler)
      • Angle
      • Constraining to slices or models
  • Interactive editor (Steve Pieper)
  • Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
    • Fast Marching demo scene
      • inner part of the tumor segmented from SPGR
      • outer part of the tumor segmented from post-Gad
      • WM and GM segmented from N4-processed SPGR (WM segmentation of the original SPGR volume is included, note under-segmented WM in the skull base)
      • all segmentations were done using FastMarching, fiducials are included for each of the segmentations
      • no fine-tuning of the fiducial locations was done -- this is an example result one can get almost right away
      • rule of thumb in placing fiducials: try to cover uniformly the volume you are trying to segment; this is particularly important for large structures like WM/GM
    • RSS demo scene
      • Segment the inner part of the tumor from SPGR using RSS
  • DTI processing (Alex Yarmarkovich, Demian Wasserman)
  • Volume Cropping (Andrey Fedorov)
  • Keyboard and mouse shortcuts (Steve Pieper)
  • Volume Rendering (Yanling Liu/Alex Yarmarkovich/Curtis Lisle)
  • EM segmentation (Kilian Pohl)

Attendees

  1. Ron Kikinis
  2. Steve Pieper
  3. UCLA DBP Engineer: Andrei Irimia
  4. Iowa DBP Engineer: Mark Scully
  5. MGH DBP Engineer: Nadya Shusharina
  6. Utah DBP Engineer: Josh Cates
  7. Utah DBP Student: Josh Blauer
  8. Utah DBP PI: Rob MacLeod
  9. Utah DBP Student: Chris Gloschat
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