You should just enter the subject names here (in this case BPD0067A, assuming this is how the subject was named for the freesurfer recon, too), and not a relative path with a directory name.
Hi Anastasia- it is attached- one note is that it is actually a .txt file but i just copied and pasted it into an RTF from our group’s cluster for this purpose.
Hi Anastasia, when running -prior, I am getting the following error:
/tmp/subj33.surfaces/BPD0067A.23694.txt: No such file or directory.
Is this something created during one of the earlier stages of preprocessing?
My corresponding output file looks like this:
INFO: SUBJECTS_DIR is /data/picsl/mackey_group/BPD
INFO: Diffusion root is /data/picsl/mackey_group/BPD/
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
trac-preproc -c /data/picsl/mackey_group/BPD//surfaces/BPD0067A/scripts/dmrirc.local -log /data/picsl/mackey_group/BPD//surfaces/BPD0067A/scripts/trac-all.log -cmd /data/picsl/mackey_group/BPD//surfaces/BPD0067A/scripts/trac-all.cmd
#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc
#-------------------------------------
#@# Priors Wed Jun 7 16:26:51 EDT 2017
Thanks
Katrina
Hi Katrina - It looks like the last stage of the pre-processing did not run for some reason. You can run that one stage only with trac-all -prior. If that runs, then you can run trac-all -path (no need to rerun trac-all -bedp).
Best,
a.y
Hi Anastasia, thanks for your response.
The entire log file is attached. Let me know if you think you need anything else.
Best
Katrina
Hi Katrina - Most likely the problem occurred earlier in the process, so the real error is hiding earlier in the log file. Can you please the entire scripts/trac-all.log file?
Thanks,
a.y
Hi all, I am running TRACULA on free surfer 6.0.0 and have done the 1st and 2nd step and am getting stuck on the last step with the following error.
Loading atlas reference volume from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
niiRead(): error opening file /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
ERROR: Could not read /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
Linux compute-0-12.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
This file is not in the dlabel/mni folder- is this because of something going wrong in the 1st and 2nd steps? Or could it be a problem with loading the atlas reference volume? I have tried this with multiple subjects and am getting the same issue
for each one.
Any help would be appreciated.
Thanks,
Katrina
Katrina Simon
Research Specialist- Mackey Lab
University of Pennsylvania Department of Psychology
(215) 573-1670
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