Hello Freesurfer Experts,

I am having a bit of trouble with the hippocampal subfield analysis using the Freesurfer 6.0 program.

My data is organized as /AnalysisFolder/Group/Subject/Anatomical/SUB_FS .. where SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ and my subject specific folder is SUB_FS. Not all data is located in /Anatomical but rather in /Group for each group.

I ran the following based on https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation:

recon-all -s ${sub}_FS -openmp 4 -itkthreads 4 -hippocampal-subfields-T1

cd $SUBJECTS_DIR/${sub}_FS/mri/
kvlQuantifyHippocampalSubfieldSegmentations.sh

This created 6 files:

lh.hippoSfLabels-T1.v10.1mm.mgz

lh.hippoSfLabvels-T1.v10.mgz

lh.hippoSfVolumes-T1.v10.txt
rh.hippoSfLabels-T1.v10.1mm.mgz
rh.hippoSfLabvels-T1.v10.mgz
rh.hippoSfVolumes-T1.v10.txt

I received the following output error in the terminal even though files were generated:

kvlQuantifyPosteriorProbabilityImages /usr/local/bin/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:217:
itk::ERROR: MGHImageIO(0xe1a620): Can't find/open file: posterior_Left-Hippocampus.mgz
/usr/local/bin/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 2000993 Aborted                 (core dumped) kvlQuantifyPosteriorProbabilityImages /usr/local/bin/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 /usr/local/bin/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 open lh.hippoSfVolumes I see the following:
Hippocampal_tail 403.806174
subiculum 309.796102
CA1 384.206539
hippocampal-fissure 143.951401
presubiculum 226.899518
parasubiculum 49.511870
molecular_layer_HP 381.834418
GC-ML-DG 196.542924
CA3 155.112708
CA4 181.563384
fimbria 31.116787
HATA 26.871413
Whole_hippocampus 2347.261836

I also found a second set of instructions for quantifying Hippocampal subfields:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

This page says to use :

quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory>

so I ran:
SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/

cd $SUBJECTS_DIR/${sub}_FS/mri/
quantifyHippocampalSubfields.sh T1-${sub}_FS test.txt $SUBJECTS_DIR/${sub}_FS/mri

No file was generated for this subject in $SUBJECTS_DIR/${sub}_FS/mri

(1)My question for kvlQuandify is if posterior_Left-Hippocampus.mgz is supposed to be created or if this is a file that was generated from a previous version of the program that is supposed to be removed from kvlQuantifyHippocampalSubfieldSegmentations.sh for Freesurfer v6.0 dev? If it is supposed to be created, I do not see this file in /mri for any subjects I tested this script on.

(2) Can I use kvlQuantifyHippocampalSubfieldSegmentations or quantifyHippocampalSubfields to calculate each individual subject's volumes for each segment generated in Freeserfer 6.0? Which is the correct program to use?

The reason for not using the whole group of subjects with one of these tools is that I want to use SPSS to correlate each subfield volume with at variety of clinical measures, however I may be using these tools incorrectly and there may be a better way to do this.

Thanks,

Ajay