Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don’t need and then I tried to run: Trac-all –intra –c <configuration file> Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original files… is there a way that I can get the script working? Many thanks. Heidi
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