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

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Simon, Katrina R [katsimon@sas.upenn.edu]
Sent: Wednesday, June 07, 2017 1:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA -path issue

Hi Anastasia, thanks for your response. 

The entire log file is attached. Let me know if you think you need anything else.


Best
Katrina 
On Jun 6, 2017, at 9:33 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

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

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Simon, Katrina R [katsimon@sas.upenn.edu]
Sent: Tuesday, June 06, 2017 3:41 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA -path issue

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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