Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
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 don¹t 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 filesŠ is there a way that I can get the script working?
Many thanks. Heidi