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!