Dear, Zoe
Usually after Freesurfer fresh install you will get a SUBJECTS_DIR with several directories, including Bert. The script you used will scan all directories under SUBJECTS_DIR and if it finds any directory without the posterior*.mgz files it will fail. You can check if this is the problem running one side from one patient like this:

cd $SUBJECTS_DIR/yoursubject/mri

kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz

This will show the volume in voxels for each subfield. If it works, you can try some alternatives:
1- Set your $SUBJECTS_DIR variable as another another path and move your subjects directories (and only these directories to this place) and run the same script you tried (kvlQuantifyHippocampalSubfieldSegmentations.sh)
2- Make a little BASH script to process just your subjects. It requires you keep your subjects in directories named following a rule you can use make an iterative loop in your script. I use subject1, subject2 but you can adapt to your needs. Something like the CalcHippoVol I attached. Before using do any adaptation you may need and make it executable (for example, with a chmod +x CalcHippoVol). Then just run from command prompt from within the directory you saved the attachment typing:

./CalcHippoVol

This way, if all works you will get 2 files, LeftVol and a RightVol, inside each of your subject/mri directory with the volumes you want. Notice that:
1- the volumes are in voxels and, despite your original voxel volume, the hippo-subfields processed by Freesurfer will be 0.5 x 0.5 x 0.5 mm. So vol(mm3)=vol(voxels)/8.
2- it is difficult to determine the precise limits of each subfield in the extreme end of the tail of the hippocampus, so the recon-all -hippo-subfield processing pipeline group all remaining voxels in the posterior_Left-Hippocampus.mgz for left hippocampus and posterior_Right-Hippocampus.mgz for right one. So these last files does not represent the whole hippocampi as the name could suggest. Check details at Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI.
Hi, Eugenio.
I would like to suggest a different name for this file. What do you think about something like posterior_left_tail_complement.mgz and posterior_right_tail_complement.mgz.
Cheers,
Marcos

Em Seg, 2013-06-24 às 16:00 -0400, Yang, Zoe escreveu:

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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