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!
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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.
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