Thanks very much!
On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < 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> 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> 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> 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 >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing >>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------------------- >>>> Juan Eugenio Iglesias, >>>> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu >>>> Athinoula A. Martinos Center for Biomedical Imaging >>>> 149 Thirteenth Street, Suite 2301 >>>> Charlestown, Massachusetts 2129 >>>> U.S.A. >>>> >>>> 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 >>>> dispose of the e-mail. >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------------------- >>> Juan Eugenio Iglesias, >>> PhDhttp://www.jeiglesias.comigles...@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.comigles...@nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, > PhDhttp://www.jeiglesias.comigles...@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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