Hi again, Raja.
Which labels and meshes to use depends on what you want to do. If you
extract all the priors corresponding to all the labels in the atlas (the
list is in $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt), you
would have a volumetric version of the atlas (rather than a mesh).
Cheers,
/Eugenio
On 08/07/2013 06:04 PM, Rajapillai Pillai wrote:
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.pil...@gmail.com <mailto:raja.i.pil...@gmail.com>> wrote:
Thanks very much!
On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias
<igles...@nmr.mgh.harvard.edu
<mailto:igles...@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
<igles...@nmr.mgh.harvard.edu
<mailto:igles...@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
<igles...@nmr.mgh.harvard.edu
<mailto:igles...@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 <igles...@nmr.mgh.harvard.edu
<mailto:igles...@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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igles...@nmr.mgh.harvard.edu
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-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
<mailto:igles...@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
igles...@nmr.mgh.harvard.edu <mailto:igles...@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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu <mailto:igles...@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
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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