View source for DTI Validation Telephone Conferences 2008

'''Tuesday March 4, 2008 - 11:00 am EST'''


'''PROGRESS:'''
*MIND DATA<br/>
Sonia has identified that the initial script run in New Mexico to start the conversion of the DWI DICOM mosaic data to nrrd format erroneously cut 4 slices of the image data away.  This is what resulted in the misregistration with the Freesurfer segmentation data and the created the problem with the acruate fasciculus ROIs.  This good to know before we get any further so we can verify that this error did not affect the brain and report back next meeting. She will need to redo the ROIs so don't work on this part of the project yet.   Jim Fallon is creating the "master neuroanatomist" hand segmentation of the tracts we are using for this project.  (Awesome JIM!)  
*PHANTOM DATA<br/>
Sonia posted Slicer tractography results from the TEEM phantom (see figure below).  John M downloaded and began processing the phantom data, but is noting some issues due to the large homogenous volume of the synthetic tract (e.g. follows inner curve of helix).  He would like to work with it more and will report results at next T-con.  Nothing from any other site.  MICCAI and other deadlines have been a major time constraint.  Discussed options for how to motivate forward progress on project, with CF suggesting more frequent email reminders and use of the wiki to document individual site progress.  
*OTHER<br/>
Randy described another approach to validating DTI tractography used by Martinos colleagues.  She will circulate the 2005 ISMRM abstract and associated website information to the group for future discussion.
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'''ACTION PLANS'''
#All groups need to process the TEEM helix data and post results by next T-con on March 18th
#Sonia will set up a wiki progress page for us  
#Randy will send first reminder to group right after MICCAI deadline 



'''Tuesday February 19, 2008 - 11:00 am EST'''


'''PROGRESS:'''
Tri's phantom data was downloaded by a few groups who were able to generate tracts from it.  No problems were encountered, but not all groups have yet attempted it.  I believe that all sites have now uploaded results for the one subject we agreed to do for the AHM meeting.  Sylvain Gouttard found an error in the ROIs posted for generating the arcuate fasiculus tract, so please disregard that until Sonia posts a corrected set of ROIs and sends out an email notice.  Nathan was not on call and no input on what the problems are with his phantom.

== '''ACTION PLANS''':  ==
#All sites PLEASE download new TEEM 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 T-con (Tuesday March 4th).
# All sites look at the results of the registration between the DTI data and structural scan for the exemplar subject (and as many as you have time for) so we can discuss any outstanding registration issues (brought up as a potential problem by Guido).




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'''Tuesday February 5, 2008 - 11:00 am EST'''


'''PROGRESS:'''
<br/>
'''DWI PHANTOM'''<br/>
[[Image:TEEMphantom.png | 400 px |right ]]
* 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 has generated and posted ROIs for the group to use for generating tractography results in the directory 'home/Projects/NAMIC_DTI_VALIDITY__0074/Data/helix_phantom_NAMIC_DTI_validity'.
<br/>
'''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 has reformatted them for the group and  posted them on the SRB in the directory 'home/Projects/NAMIC_DTI_VALIDITY__0074/Data'. 

* Randy will update the wiki to add this info to our ROI page.
[[Image:TeemPhantom-SlicerROI0001.png | 250 px | right]]

== '''ACTION PLANS''':  ==
#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).
# Nathan will work with the group to determine what problems caused tractography with his phantom to fail.  (Nathan can you please post an image of a tract you generated from the phantom using your algorithm so that everyone knows what the target outcome is?)
# 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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'''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 [http://www.na-mic.org/Wiki/index.php/Hageman:NAMICHelixPhantom 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.



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