Hello, I ran recon –all on my scans and the output files reported the following error:
SUBJECTS_DIR /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer FREESURFER_HOME /opt/freesurfer Loading source label. Invalid argument ERROR reading /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage/label/lh.BA1.label Linux dale 2.6.32-40-server #87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012 x86_64 GNU/Linux
recon-all -s AA435.C1 exited with ERRORS at Wed May 9 01:37:19 CDT 2012.
I couldn't locate the folder fsaverage: /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage
Please advise. Rashmi.
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This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
recon-all is supposed to create a symlink from the fsaverage in your /opt/freesurfer/subjects dir to you subjects dir, but sometimes this doesnt seem to work for some people. so first goto your subjects dir and check if that link is there (could be a broken link). if it isnt, then just copy the fsaverage dir from /opt/freesurer/subjects to your subjects dir (dont create a symlink).
nick
On Wed, 2012-05-09 at 20:47 +0000, Rashmi Singh wrote:
Hello, I ran recon –all on my scans and the output files reported the following error:
SUBJECTS_DIR /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer FREESURFER_HOME /opt/freesurfer Loading source label. Invalid argument ERROR reading /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage/label/lh.BA1.label Linux dale 2.6.32-40-server #87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012 x86_64 GNU/Linux
recon-all -s AA435.C1 exited with ERRORS at Wed May 9 01:37:19 CDT 2012.
I couldn't locate the folder fsaverage: /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage
Please advise. Rashmi.
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Nick Schmansky -
Rashmi Singh