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:iglesias@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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-- 
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Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
iglesias@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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