On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias <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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Juan Eugenio Iglesias, PhD
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iglesias@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
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