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:
lĂnea 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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