2008 Winter Project Week Tractography Meeting Notes
- 1 Brief Summary
- 2 Action Plans
- 3 1) ROI definitions and impact on different methods
- 4 2) Debugging
- 5 3) Review and define metrics to compare results, which methods to compare?
- 6 How to approach Test- Retest data
- 7 Milestones and dates for next steps in project
- 8 4:00- 5:00 PM NAMIC DTI module discussion
- 9 Miscellaneous Meeting Notes
"We know when the track is bad (or ugly) but we don't know when it is good." CF Westin
- All sites could analyze new dataset
- All sites could generate all requested tracks (Ugly R fornix), missing arcuate fasiculus
- ROIs still need work
- Metrics for comparison still need work
- Made lots of progress on Slicer 3 DTI integration (see below)
- Randy Gollub met w/ Dan Marcus re: data management needs of this project. Dan Marcus set up a mirror of our data repository on Central XNAT (http://central.xnat.org/, however, we will need to continue to use SRB to share image and analysis files for the next several months.
- Read this whole page and then edit to make additions and/or corrections (Guido, CF and Randy did their best to capture the contents and plans)
- Upload your presentation slides to the Workshop page (http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_Tractography)
- We will use the structure of regular bi-weekly T-cons, Tuesdays at 11 AM EST/ 9 AM MST/ 8 AM PST to continue to move this project forward.
- First T-con will be Tuesday January 22, 218-936-1100; Conference ID: 51427#
- Agenda for first T-con will be review of Nathan Hageman's helical phantom and choice of metrics for all to generate and share.
- We agreed to the milestone of analyzing the full n = 9 test/retest data set prior to Summer Programmer's week.
- Intermediate goals to be set by group in our regular T-cons.
EVERYONE READ, IF YOU SEE YOUR NAME- DO
- Upload to our SRB workspace the DTI registered (using FSL's FLIRT) Freesurfer generated white matter mask in nrrd format at same resolution as DTI data for each subject (Anastasia (her part is done already), Sylvain, bug-reporter as needed).
- Upload to our SRB workspace DTI registered additional neuroanatomical label maps for tracks (e.g. ending structures) adding arcuate fasiculus as agreed upon by clinical break-out group at 3-4 PM (Randy/Marek/Sonia).
- Upload to our SRB workspace helical phantom binary code and other materials with documentation (Nathan Hageman) and download to play with (all others)
1) ROI definitions and impact on different methods
- Force all methods to use the same ROIs or branch and have two or more classes of optimal ROIs?
- For streamline methods larger ROIs than the tract itself good
- For shortest path methods, connections stop at ROI
- Role of DTI Atlas
- Missing arcuate fasiculus
- We should all start with the same ROIs, and then allow them to be adapted to specific method, as long as that process is well-documented. Report back the modified/new ROI.
- Need to add end-points
- Randy and others will explore finding personnel and resources to generate expert neuroanatomical segmentation of the tracks.
Create/use existing synthetic tensor data set (Gordon's helix, crossing fiber situation). Good for debugging algorithm method comparison. Nathan Hageman w/input from other algorithm teams will generate helical synthetic data set. What outcome metrics from it will each team generate?
3) Review and define metrics to compare results, which methods to compare?
Current metrics: tensor invariants (FA, trace, mode, norm), volume, length.
- Binary mask is needed for volume calculation. How do we generate binary masks and choice of threshold is a part of the method.
- Possibility to include weights to voxels inside the mask.
- Overlap metrics can be used to compare methods with different spatial extent. Need to send the binary masks to Sonia to do such calculations.
- Masks allow us to look at distribution of measures
- Concentrate on two tracts?
- Parameter settings within a method may change the results comparable to the difference between methods.
- Bundle thickness: mix of radius of tract and uncertainty
- How to define volume from connectivity map (shortest path, or stochastic)
- Quantification of registration error and its propagation forward and impact on final results
- Agree on units for volume measures. Suggest cubic centimeters (ml) vs mm3
How to approach Test- Retest data
Never even started discussion of this topic!
Milestones and dates for next steps in project
Registration &/or resampling to support visit 1- visit 2 analysis and group analysis
Should we make plans for a NAMIC sponsored MICCAI event: Tractography Grand Challenge e.g. the one done last year for segmentation? See http://mbi.dkfz-heidelberg.de/grand-challenge2007/)
4:00- 5:00 PM NAMIC DTI module discussion
The NAMIC DTI module should include a comprehensive set of modules that allow users to efficiently explore, process visualize and analyze diffusion imaging data. This breakout session first discussed the status of each Core-1 site w.r.t. integration of tools to Slicer-3, and then contrasts this list with the current status of the Slicer-3 DTI module and with the plan for future Core-2 developments.
- Each Core-1 DTI development site: Status Slicer-3 Integration
- Utah-I (Tom Fletcher/ Ross Whitaker): Volumetric connectivity ready as command-line procedure, only needs a wrapper for Slicer-3 / Current activity: EPI and Eddy-current correction based on field maps (will collaborate with C-F Westin).
- Georgia Tech (John Melonakos/ Alan Tannenbaum): Geodesic Tractography Segmentation ready as command-line procedure, only needs a wrapper for Slicer-3.
- Utah-II (Casey Goodlett/ Guido Gerig): Library of tensor estimation modules / modules for mapping/resampling tensor fields (activity for ITK modules to be synchronized with Francois Budin/Sylvain Bouix) / group-wise population analysis available as batch process but needs NAMIC-compatible framework for group-wise registration of populations of images. Collaboration with MIT (Serdar Balci, Polina Golland) on integration of atlas building method with DTI population analysis. / Fiber bundle editing/postprocessing/parametrization: FiberViewer might be operated as command-line tool with wrapper. Collaboration with engineering core (Alex Yarmarkovich, Steve Pieper) w.r.t. full integration of editing into Slicer-3.
- Harvard (Tri Ngo, C-F Westin): Filtering modules and stochastic tracking available / Work towards full integration into slicer, e.g. by pull-down menue to select different tractography procedures.
- UCLA (Nathan Hageman): Helix 3-D tensor phantom to test correctness of different DTI processing methods / Development of fluid-mechanics-based tractography as standalone ITK module, requires parallel processing and interactive visualization / Development of processing for diffusion spectrum imaging (DSI) / analysis of ODFs.
- Contrasting plans of Core-1 with future development plans as identified by the Engineering Core (Alex Yarmarkovich and Steve Pieper)
- Slicer-3 DTI future plans listed at: Slicer3 DTI status
- nifty to nrrd: in progress by engineering core
- The new mBIRN compliant DTI data from MIND used for the tractography comparison used the following preprocessing steps: a) Registration (FLIRT for DTI to structural MR), b)EPI distortion correction (we used FUGUE), ITK?
It will be a priority to develop these preprocessing functions within Slicer-3: Registration became available this Jan. 2008: See update by Stephen Aylward in AHM Registration breakout session: Slides:  / Eddy-current and EPI correction see plan by Westin/Fletcher/Whitaker above.
The DTI workshop group concluded that the list provided by Alex matched deliverables proposed by developers very well.
- Action plan Core-1 and Core-2 interaction:
Core-2 teams will visit Core-1 developers for face-to-face discussion of transfer and integration of tools. It was decided in a separate meeting that first, the Utah groups will host the engineering Core-2 people for discussing Slicer-3 integration, including DTI module transfer.
Miscellaneous Meeting Notes
From Casey's presentation: Made suggestion of using one set of ROI specifications for an entire study in atlas space, mapping them back to the individual subjects.
From John's presentation: His method required that he had to shrink the provided ROIs for uncinate fasciulus and corpus callosum to make his method work. Then could generate fiber volumes for each tract. His tracts all STOP at ROIs (end points). If given ROIs farther apart could generate longer tracts. Needed a white matter mask- created his own with Tri by thresholding FA (>0.15). Discussion regarding whether the ROIs based on Susumu Mori's criteria would actually be optimal or even work for every method.
From Tri's presentation: Able to generate all tracks with given ROIs. Needed white matter mask (see above). 30 minutes/tract on 63GB computer. Seed with source, filter with sink. Had to cut uncinate fasciulus. For later statistical analysis, considered only non-zero connectivity value voxels. Reminds us that bundle thickness is related to both uncertainty and physical radius.
From Vince Magnotta's presentation: GTRACT works well for forceps major and minor, internal capusule. A Fast Marching algorithm is better for fornix, hippocampus-cingulum and cingulum. For the Fast Marching algorithm, modified the algorithm to use cost image generations based on tensor and anisotropy, gradient descent. His algorithm would perform "better" for core of cingulum bundle, needs a smaller, more focal ROI. For uncinate, couldn't get it to bend around, would need intermediate ROIs.
From Sonia's preliminary cross-algorithm study:
- rank order of qualitative accuracy (strongly underscores need to clarify the clinical goal of the tractography results)
Comments from Carlo:
- Commended us for making effort against this tough problem and for the decision to control pre-processing steps
- What is the impact of adjusting parameters within an algorithm on the outcome metrics? May need to explore this in addition to the cross algorithm assessments.
- What is the effect of the tissue properties that surround the track on results within and across algorithm.
- Differences due to the topology, how to visualize? Binary masks in/out of track volume.
Questions from Steve Pieper:
- Please point me to example NIfTI DWI/DTI datasets for testing. How is measurement frame handled in diffusion NIfTI?
- Please provide examples of data where header is corrupted going from/to FSL tools
- What interactive 3D Widgets are most needed?
- What CFD features does Nathan need for his techniques?