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 mailto: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.gzAlso, 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 trapWhat 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, /EugenioThanks very much for your time, Raja _______________________________________________ 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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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.