Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 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:
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-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