Final question regarding this: what combinations of labels and meshes should I use? Should I do all combinations between labels and positions, matching labels/positions only, etc? How can I tell which meshes correspond to what labels/areas?
Thanks for your time, Raja
On Wed, Aug 7, 2013 at 4:26 PM, Rajapillai Pillai raja.i.pillai@gmail.comwrote:
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,
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, PhDhttp://www.jeiglesias.comiglesias@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, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.