Hi again,
Zoe, Marcos is right about the fact that the script fails if the
posterior*.mgz are not found in any
1- Set your $SUBJECTS_DIR variable as another another path and move
your subjects directories (and only these directories to this place)
and run the same script you tried
(kvlQuantifyHippocampalSubfieldSegmentations.sh)
Rather than moving the subjects, I'd create symbolic links, but this is
certainly an option.
Another option is to modify
kvlQuantifyHippocampalSubfieldSegmentations.sh, replacing the two
instances of:
doIt "kvlQuantifyPosteriorProbabilityImages $compre....."
by
cmd="kvlQuantifyPosteriorProbabilityImages $compre....."
eval "$cmd"
Cheers,
/Eugenio
Em Seg, 2013-06-24 às 16:00 -0400, Yang, Zoe escreveu:
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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igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
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