No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything without
skipping steps. This will create all the files that are expected to be
there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
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-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@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
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