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 <[email protected]>wrote: > Thanks very much! > > > On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < > [email protected]> 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 < >> [email protected]> 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 < >>> [email protected]> 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 < >>>> [email protected]> 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 >>>>> [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------------------------- >>>>> Juan Eugenio Iglesias, >>>>> PhDhttp://[email protected] >>>>> 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://[email protected] >>>> Athinoula A. Martinos Center for Biomedical Imaging >>>> 149 Thirteenth Street, Suite 2301 >>>> Charlestown, Massachusetts 2129 >>>> U.S.A. >>>> >>>> >>> >>> -- >>> ------------------------------------------------------------------------------------- >>> Juan Eugenio Iglesias, >>> PhDhttp://[email protected] >>> Athinoula A. Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, Massachusetts 2129 >>> U.S.A. >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing >> [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, >> PhDhttp://[email protected] >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> >
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