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 [ | + | **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= | ||
| 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 | ||
| − | *Comply with [ | + | *Comply with [https://www.slicer.org/wiki/Documentation-Rons-Rules-For-Tools Rons Rules for Tools] |
*Registration (Dominik Meier, Hans Johnson) | *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): | **Resample as needed (DTI, T2 Baseline): | ||
***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']] | ***transforms available here: [[Projects:RegistrationLibrary:RegLib_C33|'''Reg.Lib Case 33''']] | ||
*Compareview (Jim Miller) | *Compareview (Jim Miller) | ||
| − | *Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) | + | *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] | *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] | ** [[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials tutorial]] and [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Data] | ||
| Line 46: | Line 52: | ||
***Passing Fiducials to Command Line modules | ***Passing Fiducials to Command Line modules | ||
***Fiducial Seeding | ***Fiducial Seeding | ||
| − | ** [ | + | ** [https://www.slicer.org/wiki/Modules:Measurements-Documentation-3.6 Measurements] |
***Ruler (put down two fiducials, Control-m to make a ruler) | ***Ruler (put down two fiducials, Control-m to make a ruler) | ||
***Angle | ***Angle | ||
***Constraining to slices or models | ***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) | ||
| − | ** [[Media: | + | ** [[Media:AHM2011_FastMarching_demo.tgz|Fast Marching demo scene]] |
*** inner part of the tumor segmented from SPGR | *** inner part of the tumor segmented from SPGR | ||
*** outer part of the tumor segmented from post-Gad | *** outer part of the tumor segmented from post-Gad | ||
| Line 59: | Line 67: | ||
*** no fine-tuning of the fiducial locations was done -- this is an example result one can get almost right away | *** 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 | *** 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) | *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 Yarmarkovich/Curtis Lisle) | + | *[https://www.slicer.org/wiki/Modules:VolumeRendering-Documentation-3.6 Volume Rendering] (Yanling Liu/Alex Yarmarkovich/Curtis Lisle) |
| − | *EM segmentation (Kilian Pohl) | + | *[https://www.slicer.org/wiki/Modules:EMSegmenter-3.6 EM segmentation] (Kilian Pohl) |
=Attendees= | =Attendees= | ||
Latest revision as of 17:09, 10 July 2017
Home < 2011 Winter Project Week:Breakout Slicer with RonBack 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
- 10 minutes or less per segment
- Comply with 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: Reg.Lib Case 33
- Resample as needed (DTI, T2 Baseline):
- transforms available here: Reg.Lib Case 33
- 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
- Fiducials tutorial and Data
- 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
- Fast Marching demo scene
- 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
- Ron Kikinis
- 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
