Mbirn: Morphometry BIRN Meeting, June 7 2006, Teleconference

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Home < Mbirn: Morphometry BIRN Meeting, June 7 2006, Teleconference
  • Announcements
    • Greg Farber is now the NCRR Program Officer for all of BIRN (email: farberg@mail.nih.gov)
Participants:
 MGH: B. Rosen, R. Gollub, D. Kennedy, K. Helmer, B. Fischl, S. Murphy, R. Buckner
 BWH: S. Pieper
 JHU: A. Kolasny
 UCSD: A. Dale, C. Fennema-Notestine
 Duke: J. MacFall, A. Song
 UCLA: A. Toga
 UCI: no one
 MIT: no one
 WUSTL: D. Marcus
 NCRR: G. Farber
  • NCRR Update

Greg Farber introduced himself and gave an outline of his background.


  • Update on Greg Farber Visit to MGH on June 6, 2006 by Bruce Rosen

Funding for years 4 and 5 are up for review. The date for the decision about the continuation of funding has been moved up to the NCRR council meeting in October. With that in mind, we need to have a clear set of deliverables and prioritize future work in preparation for that meeting. Bruce Rosen thought that the report for the October meeting should be in a near final state by the 1st or 2nd week of October. Greg Farber will work with mBIRN on this report. Greg Farber will distribute a document in early July that will lay out NCRR expectations for the coming period.

Karl Helmer will post a timeline for the October report on the wiki page. It is imperative that each group document their progress on the wiki pages as this material will be used to prepare the October report and by Greg Farber to follow the progress of mBIRN work.


  • Diffusion Tensor Imaging

Karl Helmer updated the group on the 3 site (JHU, Duke, MGH) DTI calibration study. The protocol has been decided upon. Both the Duke and MGH sites will acquire data that is equivalent to the data acquired by JHU in their initial DTI calibration study. This data will be used to determine reproducibility across sites. Allen Song mentioned that Duke has approved the release of his eddy-current correction software for diffusion-weighted data to MGH and the paperwork is to follow.

This work is proceeding in harmony with the fBIRN group who will begin to acquire DTI data along with their structural and functional scans. In keeping with this goal to achieve multi-modal integration, the DTI sequence and analysis methods have been submitted to the fBIRN IRB Working group for inclusion in the new acquisition protocol. Karl Helmer will forward detailed protocol and consent form to the JHU site for them to make site-specific changes.

Anders Dale updated the group on the tensor reorientation tool that his group and Mike Miller's group have been working on. VETSA data will be used for testing and will be processed with this tool. He noted that this tool will be made publicly available though BIRN. There was discussion on the need for this tool to be part of a workflow, be released as stand-alone code, or both. Karl Helmer will follow up with Anders Dale to determine the deliverables.

Steve Pieper updated the group on progress of the NRRD format effort. Jonathan Farrell (JHU) is working on modifying their software tools to accept NRRD headers. Gordon Kindlmann will be on the NIfTI task force that is working on defining headers for diffusion-weighted imaging data.


  • Databases and Workflows

Further definition of the FreeSurfer-LDDMM web-services project is needed. Karl Helmer will organize a workflows meeting to define deliverables. The group will include Shawn Murphy, Anders Dale, Chris Fenema-Notestine, Anthony Kolasny, and Mike Mendis.

Dan Marcus noted that the XNAT paper has been submitted and is in revision. In addition, the XNAT website (www.xnat.org) is live and XNAT can be downloaded from the website. Glenn Hoffman has been hired as the XNAT rollout specialist and will be based at Harvard. The XNAT work will be divided into two categories: 1) roll-out to be focused on by Randy Buckner's group and 2) development to be focused on by the WUSTL group. JHU and Duke are also XNAT test sites and are working with the developers. In addition to local instances of XNAT, the development group will work on making a XNAT - HID connection. This will be a deliverable for October. Karl Helmer will schedule a session at the October BIRN AHM in which users could interact with XNAT personnel to discuss use cases. James MacFall mentioned that they would like to put the ELUDE and MIRIAD data into XNAT. The SASHA data also could also be share-able.

Steve Pieper discussed the BIRN-ID generating software. There are no code-related issues that would prevent the distribution of this software. The software uses the patient ID and the site code to generate a unique ID number. Karl Helmer will work with Steve Pieper and the BIRN-CC to put this software up on the BIRN Downloads page.

There was general discussion of data that would be appropriate for inclusion in the BIRN databases. The large NIH pediatric data set will be available in July, but the release conditions for that data were unknown. Anders Dale noted that the ADNI imaging data is available in DICOM format, but that one has to apply as an investigator to get access. Anders Dale's group is currently processing roughly half of the ADNI data and should be finished by October. This data would not be available through BIRN until the data sharing issues are worked out. Since there was no ADNI money allocated for the processing of the data there was some discussion of going after this as a BIRN deliverable, with MGH possibly processing the other half of the data. Greg Farber has agreed to help us identify a funding source for this.


  • Other Reports

Steve Pieper - BWH has been working on building atlases using DTI data.

Dan Marcus - The OASIS data set paper will be finished in July and the data available for distribution. Anders Dale volunteered to have his group do the FreeSurfer processing; the MGH group volunteered as well.

Anthony Kolasny - reported that the Teragrid processing is finally finished and took ~240,000 CPU hours. They are currently working on 200 (of 40,000) outlier data sets, but that that should be finished in the near future.

Allen Song - reported that his group is working on the problem of eddy-current distortion correction for SENSE imaging. There will be a comparison between the Dale and Song methods of eddy-current correction. Anders Dale noted that GE is working on incorporating the UCSD method into GE software. Allen Song also noted that they are working on a standardized pipeline of acquisition parameters and data format for diffusion MRI data.

James MacFall - reported that they are making progress on their segmentation software; they would like to tie into the LDDMM hippocampal segmentation and compare their results with those of JHU.

Arthur Toga - reported that he and Bruce Rosen will be meeting to discuss the sharing of the ADNI data. Work on the UCLA workflows will be accelerated and UCLA will work on making sure that what they are doing and what is being done at MGH are integrated.

Chris Fenema-Notestine - reported that their lexicon has been incorporated into Protege.


It was decided that another t-con will be held late July. Karl Helmer will schedule this.

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