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. > >
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