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 Lab
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