Hi

kvlQuantifyHippocampalSubfieldSegmentations.sh "expected that the "-hippo-subfields" flag has been used for each subject in $SUBJECTS_DIR; if this is not the case the "kvlQuantifyHippocampalSubfieldSegmentations.sh" script will fail and no (or incomplete) output files will be generated". from http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation.

Cheers Knut J

On 08/30/2012 07:56 PM, Carolina Valencia wrote:

Hi Freesurfer community:

I run hippocampal subfields command succesfully

recon-all -s CORBIC_vol15 finished without error at Thu Aug 30 11:29:16 COT 2012 done

but when I run kvlQuantifyHippocampalSubfieldSegmentations.sh

the terminal shows some errors:

resultsDirectory /home/cvalencia/freesurfer/subjects/volumetria cd /home/cvalencia/freesurfer/subjects/volumetria resultsDirectory /home/cvalencia/freesurfer/subjects/volumetria startIndex: 1 endIndex: 5 cd CORBIC_vol15/ Quantifying subject CORBIC_vol15/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /home/cvalencia/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 cd .. Quantifying subject CORBIC_vol15/ right Doing right side cd mri kvlQuantifyPosteriorProbabilityImages /home/cvalencia/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt cd .. cd .. cd fsaverage/ Quantifying subject fsaverage/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /home/cvalencia/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(0x9231728): Can't find/open file: posterior_Left-Hippocampus.mgz /home/cvalencia/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: línea 22: 15068 Abortado (`core' generado) kvlQuantifyPosteriorProbabilityImages /home/cvalencia/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 /home/cvalencia/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

when I tried to visualize them

cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/CORBIC_vol15$ freeview nu.mgz \

...

-p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt

freeview.bin: No match.

Am I miss something?

Best regards,

-- *Carolina Valencia M*

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