Hi,
I'm experiencing a problem when running the automated hippocampal subfield segmentation script. Unfortunately, I have been unable to determine the cause of the error. After reconstructing all participant data with the -hippo-subfields flag, I ran the "kvlQuantifyHippocampalSubfieldSegmentations.sh" script. The script seems to be working fine, generating subfield values for all participants until the very end when it attempts to generate the stat tables (I think). At this point, I receive the following error:
/Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt
I've copied some output and the error message below, including the last participant in our folder it runs through before attempting to generate volume stats.
Thanks for any help you can offer!
Best
Erin
-- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Labhttp://www.psychiatry.wisc.edu/abercrombie/ 6001 Research Park Blvd. Madison, WI 53719 edubwalsh@gmail.com
Relevant information:
FREESURFER_HOME: /Applications/freesurfer
Current working dir ran command: /Applications/freesurfer/subjects/CORTMR/recon
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
Kernel info: Darwin 12.4.0 x86_64
Command line ran: kvlQuantifyHippocampalSubfieldSegmentations.sh
Output/Error (after seemingly generating hippocampal subfield values for all participants):
... cd 228/ Quantifying subject 228/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt cd .. Quantifying subject 228/ right Doing right side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4_DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt cd .. cd .. cd fsaverage/ Quantifying subject fsaverage/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt