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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