Can you send your configuration file? ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Simon, Katrina R [katsi...@sas.upenn.edu] Sent: Wednesday, June 07, 2017 4:43 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA -path issue
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 On Jun 7, 2017, at 3:58 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Simon, Katrina R [katsi...@sas.upenn.edu<mailto:katsi...@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 <ayend...@mgh.harvard.edu<mailto:ayend...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Simon, Katrina R [katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>] Sent: Tuesday, June 06, 2017 3:41 PM To: Freesurfer@nmr.mgh.harvard.edu<mailto: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 katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu> (215) 573-1670 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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