Mbirn: Multi-site Imaging Research in the Analysis of Depression (MIRIAD) Project

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Multi-Institutional Research in Analysis of Depression (MIRIAD)

  • Background: The MIRIAD is a collaborative application aimed at developing a morphometry pipeline that integrates multi-site neuroimaging analysis tools that process MRI data typically acquired for detecting white matter lesions (T2- and proton density MRI). To drive the application we attempted to extend the analysis of retrospective depression data from the Duke site, which had been previously analyzed using only manual segmentation methods. This data was further processed using registration, atlas generation and segmentation tools from the BWH and UCLA sites.

UPDATES

2005.07.21 (J. Jovicich)

  • Teleconference: J. Grethe, S. Pieper, B. Boyd, S. Gadde, J. MacFall, J. Jovicich
  • Action items:
    • Jeff will move MIRIAD's Oracle metadata into Duke's MIRIAD database. The HID-GUI that Duke will visualize this with shall be the latest GUI version (which Jeff hasn't tested on the MIRIAD HID at BIRN CC).
    • James will send a copy of the MIRIAD manuscript to Jeff, who will use it as reference for defining sample queries.
    • Jeff will send to James & Jorge the web links to sample public data/tool distribution pages. These shall be used as starting points for defining the technical information, license (if any), acknowledgement requests, etc. that will accompany the data
    • This group will meet next week to follow up progress at Duke's side after Jeff moved the data.
  • Discussion topics:
    • Duke database updates (S. Gadde): rack upgraded July 6-10. The database was restored afterwards. The database has a new user (miriadweb) and a blank HID for the MIRIAD data. I have also reinstalled our local GUI. It currently points to the fBIRN data or MIRIAD data depending on the user who logs in. Brian has username/password to miriadweb. His 'edit' permissions will be removed since that shouldn't be necessary for this dataset.
    • Once both are up, there shouldn't be any difference from users' perspective between the firewalled Duke-MIRIAD-HID and the public BIRN CC-MIRIAD-HID.
    • The scripts that insert information from the SAS tables into the HID can't be fully generalized for arbitrary sites, but James can use them to later create the extended 1,200 HID.
    • The 1,200 brain dataset might be a good testcase for workflow applications. The HID will have to be expanded to include the parameter space to explore under various processing cases. The HID-GUI will have to be expanded to capture this information in queries

2005.07.18 (J. MacFall, J. Jovicich)

  • Outstanding unsolved issue: BIRN CC and Duke HID-GUI infrastructure to support public distribution of MIRIAD and later a much larger dataset (1,200 brains, controls, unipolar depression, several timepoints). Validation of de-facing tool would support it's use for de-identifying this larger dataset.
  • MIRIAD paper was resubmitted to Neuropsychopharmacology on 6/27/05. There were critics on repairable things (more details requested) and there was a critic about the statistical analysis approach, which with very distributed lesions had very few lesions over ROIs. The paper was resubmitted with minor changes.
  • Database infrastructure for MIRIAD dataset still incomplete.
    • We want to make the MIRIAD dataset publicly available
    • Because of Duke's hospital firewall issues, a Duke-served HID GUI would not be accessible outside Duke.
    • In early June Jeff Grethe proposed a solution in which a BIRN CC served HID GUI is used for public access and a Duke-served HID is used for subject management. Unclear about progress.
  • James is willing to then use the MIRIAD distribution infrastructure to make publicly available the larger dataset (1,200 brains, controls, unipolar depression, several timepoints) of which MIRIAD is a subcomponent. These data would have to be de-identified, potentially using our de-facing tools.

2005.05.17 (J. MacFall, S. Pieper)

  • A journal paper has been submitted, no news yet on the review.
  • Previous MIRIAD pipeline to be updated with new Expectation Maximization (EM) algorithm developed by Kilian Pohl. Tentative plan of analysing full Duke dataset (1,200 subjects control and depressed subjects, multiple time-points).
  • Waiting for Susumu's white matter atlas to start study that co-registers the tractography atlas to the control/depression data and study correlation between volume and number of white matter lessions associated with particular tracts (left/right uncinate, left/right longitudinal fusiculus).
  • NEED: i) to get MIRIAD-HID at Duke from BIRN CC; ii) work plan to decide which dataset to process next and for what purpose; iii) work plan to decide how or if this pipeline can be made available in a more user friendly way including the LONI lobar atlas component, iv) review Oct 2005 goals

2005.02.11 (J. MacFall)

  • Progress on MIRIAD has finally resulted in a manuscript. It only needs some editing by David Rex since the lobar atlas that he created has not been published before. I expect to send the manuscript to the co-authors next week for initial review, minus David Rex's final editing and then a final copy whenever he can finish. He is heavily committed to his medical work at UCLA, but he has assured me he can do his section.
  • The MIRIAD work was successful enought that we are planning to process a much larger number of our cases as part of the mBIRN work at Duke to produce further papers.
  • James will contact Steve Pieper to push forward improvements on the EM component of the MIRIAD pipeline. They will try to discuss this before or at Miami at the latest.
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