Did you run recon-all -subjid bert -hippo-subfields? If so, there should be a log file with the output from the hippo-subfield code in $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it to get an idea of what happened. Kind regards, /Eugenio

On 07/31/2013 04:38 PM, Rajapillai Pillai wrote:

Thanks very much for the prompt response. The command I ran was

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

in $SUBJECTS_DIR/bert/mri

And yeah, it's not in the mri directory. Any idea what might have gone wrong and how I can try and fix it?

Thanks, Raja

On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu mailto:iglesias@nmr.mgh.harvard.edu> wrote:

Hi Raja,

...

I'm have a question regarding the GEMS hippocampal segmentation.
I saw on the wiki how to run -hippo_subfields, but how do I
access the atlas itself? What file is it under.

That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz

...

Also, I'm not sure if I'm missing some files: whenever I try to
do one of the individual commands using, for example,
posterior_Right_Hippocampus.mgz, it gives the following error:

volumeInVoxels:
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file:
posterior_Right-Hippocampus.mgz
Abort trap

What command is this? In any case, it's pretty clear that the file
is missing....

...

Also, upon searching through my freesurfer directory, I cannot
find any posterior_Right-Hippocamus.mgz or
posterior_Left-Hippocampus.mgz files.

It should be under the "mri" directory. If it isn't, there was
some problem running the algorithms.

Cheers,

/Eugenio

...

Thanks very much for your time,
Raja


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