Difference between revisions of "2011 Winter Project Week:Breakout Slicer with Ron"
From NAMIC Wiki
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***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 | + | *Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) |
*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] | ||
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*** 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 | ||
| − | *DTI processing (Alex | + | *DTI processing (Alex Yarmarkovich, Demian Wasserman) |
*Volume Cropping (Andrey Fedorov) | *Volume Cropping (Andrey Fedorov) | ||
*Keyboard and mouse shortcuts (Steve Pieper) | *Keyboard and mouse shortcuts (Steve Pieper) | ||
Revision as of 17:34, 3 January 2011
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
Preliminary Program
- 10 minutes or less per segment
- Comply with Rons Rules for Tools
- Registration (Dominik Meier, Hans Johnson)
- Register everything to the SPGR data: complete. Data, transforms and instructions available here: Reg.Lib Case 33
- additional info:
- basic concept and outline of DTI registration (cookbook) on FAQ, incl. List of special caveats pertaining to DTI registration and resampling
- overview of all DTI cases currently in the registration case library
- similar cases that required different approaches Case 29: DWI -> T2 -> T1 (direct to T1 fails), Case 03: low resol. & anisotropy require resampling, masking & manual initial alignment, Case 27: anisotropy required prior DWI resampling prior to conversion
- Resample as needed (DTI, T2 Baseline):
- transforms available here: Reg.Lib Case 33
- Compareview (Jim Miller)
- Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich)
- 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
- 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:
- Utah DBP Engineer: Josh Cates
- Utah DBP Student: Josh Blauer
- Utah DBP PI: Rob MacLeod
- Utah DBP Student: Chris Gloschat
