Dear Eugenio, Thanks for the reply. Yes, we created a test directory containing two subjects that have been reconed with the -hippo-subfields flag. Both of them have 20 output files. Cheers, Zoe
From: Juan Eugenio Iglesias [mailto:igles...@nmr.mgh.harvard.edu] Sent: Monday, June 24, 2013 5:03 PM To: Yang, Zoe Cc: 'Freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh Dear Zoe, have you checked whether all directories within your subject directory correspond to subjects which have been reconed with the -hippo-subfields flag? Cheers, /Eugenio On 06/24/2013 04:00 PM, Yang, Zoe wrote: Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We did use the -hippo-subfields flag for all of our subjects first, and the output was 20 left and right subfield mgz files (it completed without any errors). The subjects had already undergone the standard volumetric FreeSurfer pipeline and therefore we ran the command: recon-all -s subjectID -hippo-subfields. The error message for kvlQuantifyHippocampalSubfieldSegmentation that I'm getting is: resultsDirectory ***/HIPPOCAMPAL_TEST cd ***/HIPPOCAMPAL_TEST resultsDirectory ***/HIPPOCAMPAL_TEST startIndex: 1 endIndex: 2 cd subjectID_recon/ Quantifying subject ID_recon left Doing left side cd left cd segmentationWithoutPartialVolumingLog 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 terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: posterior_Left-Hippocampus.mgz kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap 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 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 Is there anything else that we are missing and should run? Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu<mailto:igles...@nmr.mgh.harvard.edu> Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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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