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<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwa...@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
_______________________________________________ Freesurfer mailing list 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.
