Thanks very much!On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu> wrote:
Shame on me; there's a way of doing this. You need a reference volume; for the hippocampal subfield atlas:
$FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz
the reference volume would be:
$FREESURFER_HOME/data/GEMS/imageDump.mgz
The command would be:
kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz [labelNumber] [meshNumber]
"meshNumber" is the index of the mesh to extract in the collection; use -1 for the reference position.
labelNumber is the label whose probability map you want to rasterize ( 0 = white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt).
From the volumetric rasterized prior probability map, you can easily compute volumes, if you want.
Cheers, and sorry again for the original wrong answer,
/Eugenio
On 08/07/2013 01:30 PM, Rajapillai Pillai wrote:
Hi again!
I have another question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection?
Thanks a lot,Raja
On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu> wrote:
Sounds good, but please email the list, rather than only me ;-)
/E
On 07/31/2013 05:03 PM, Rajapillai Pillai wrote:
Thanks a lot. I'll let you know if I have any more issues.
Best regards,Raja
On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu> wrote:
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> wrote:
Hi Raja,That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz
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.
What command is this? In any case, it's pretty clear that the file is missing....
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.mgzAbort trap
It should be under the "mri" directory. If it isn't, there was some problem running the algorithms.
Also, upon searching through my freesurfer directory, I cannot find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files.
Cheers,
/Eugenio
Thanks very much for your time,Raja
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-- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
-- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.