DTI Validation Telephone Conferences 2008

Tuesday January 22, 2008 - 11:00 am EST

PROGRESS:

• Nathan has posted both a 6 gradient direction phantom and a helical phantom that simulates a 60 gradient DWI acquisition mirrors the MIND Reliability dataset. Both are now available on the BIRN portal along with a document with a description of the different files present and how to use them is in the phantom directories:

/home/Projects/NAMIC_DTI_VALIDITY__0074/Data/helix_phantom_NAMIC_DTI_validity/

Both are in analyze format. Nathan is working to transform them into nrrd format, any help would be gratefully appreciated.

• Once they are in nrrd format, Sonia will generate the Regions of Interest and post those ASAP.

• Nathan is creating a wiki page with complete description of the phantom methods and link to download the binary.

• Anastasia has uploaded the transformed masks and segmentations for the MIND Reliability subjects into the Data directory:

freesurfer_segmentations_whitemattermasks_xformed_to_corrected_dwi_visit1_all_subjects.tar.gz

and the transformation matrices: freesurfer_to_corrected_dwi_visit1_xform_matrices_all_subjects.tar.gz

One could now start with the original segmentations, which are under freesurfer_results, and apply these matrices to resample to the corrected DWI visit 1 data.

• Jim Fallon has has accepted an invitation to work with the Clinical team (Randy and Marek) to define and generate the additional ROIs and neuroanatomical landmarks for the tracts that we agreed upon at the AHM. They will be working together on Friday Feb 1 in Boston and will report progress on next T-con.

ACTION PLAN:

All sites download the new phantom data (in nrrd format w/ROIs) on Monday and run your tractography algorithm on it before next Tuesday's T-con. Use this email list to work out any logistical problems.

Tuesday February 5, 2008 - 11:00 am EST

PROGRESS:
DWI PHANTOM

• Many sites were able to download Nathan's phantom data, but none could generate reasonable tractography results.
• Nathan was unable to join our T-con due to illness but has since been appraised of the situation and is in agreement with the group plan.
• Tri volunteered and has completed generating another phantom using the TEEM software. The group agreed that he would use a simple unity measurement frame, isotropic voxels, match the MIND data where possible, add "some" noise.
• Tri has already uploaded the phantom data (dwi and dti images and a "white matter mask") and given our group permission to view it on our SRB space in a directory called "home/Projects/NAMIC_DTI_VALIDITY__0074/Data/helix_phantom_NAMIC_DTI_validity".
• Sonia will generate and post ROIs for the group to use for generating tractography results.

MIND DATA ANALYSIS

• Marek, Randy and Sonia met with Jim Fallon on Friday Feb.1st. With Jim's help we developed Freesurfer based methods to make cortical gray matter target ROIs for our tracts. The group agreed that we would start with a single tract, the arcuate fasiculus to test our outcome measures. The "source" is the inferior frontal gyrus and adjacent sulcus, the "sink" is the superior temporal gyrus and adjacent sulcus as delineated by the original Freesurfer cortical parcellation scheme. See Automatically Parcellating the Human Cerebral Cortex, Fischl, B., A. van der Kouwe, C. Destrieux, E. Halgren, F. Segonne, D. Salat, E. Busa, L. Seidman, J. Goldstein, D. Kennedy, V. Caviness, N. Makris, B. Rosen, and A.M. Dale, (2004). Cerebral Cortex, 14:11-22.
• We agreed to generate these two ROIs for the first sample subject and to "grow them" out into the underlying white matter so that algorithms such as stochastic tractography that need white matter targets can use the same ROIs.
• Randy and Anastasia generated the initial ROIs as requested in Freesurfer and Sonia is now reformatting them for the group and will post them on the SRB.
• Randy will update the wiki to add this info to our ROI page.

ACTION PLANS:

1. All sites download Tri's new phantom data (in nrrd format w/ROIs) ASAP and run your tractography algorithm on it, and upload your results (tract fields and matricies) before next Tuesday's T-con (Tuesday Feb. 19th).

Use this email list to work out any logistical problems.

1. Nathan will work with the group to determine what problems caused tractography with his phantom to fail. Request for you to post an image of a tract you generated from the phantom using your algorithm so that everyone knows what the target outcome is.
2. TWO SITES STILL NEED TO UPLOAD TRACTOGRAPHY RESULTS FROM VISIT 1 OF THE SAMPLE MIND DATA- YOU KNOW WHO YOU ARE!!!!

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