i dont know the answer to your question, but there have been some bug fixes to the hippocampal fields stuff since the 5.1 release. i've posted tarballs of the relevant executables here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/
in these directories, corresponding to the 32b-linux, 64b-linux and mac os platforms:
linux-centos4/kvl_centos4.tgz linux-centos4_x86_64/kvl_centos4_x86_64.tgz macos-leopard-intel/kvl_leopard.tgz
get the tgz file for your platform and copy it to your $FREESURFER_HOME/bin directory, then type:
cd $FREESURFER_HOME/bin tar zxvf <filename>
to extract the files (where <filename> is the .tgz file you downloaded). you might also need to run:
chmod a+x kvl* chmod a+x recon-all
i dont know if it will fix the problems you are encountering, but it is certainly worth the effort to update as it addresses some known problems.
n.
On Wed, 2011-11-16 at 09:42 -0500, Alan Francis wrote:
Hi FreeSurfer folk:
I have a question that is in the same vein as Marie's. Should not the sum of the Hippocampal subregional volumes be = total hemispheric Hippocampal volume?
thanks,
Alan
On Wed, Nov 16, 2011 at 2:52 AM, Marie Schaer Marie.Schaer@unige.ch wrote:
Hi all, I just ran the hippo-subfield segmentation on a batch of subjects. Everything went perfect for most of my subjects, however I got an outlier in the left CA1 for one subject who had a very large volume. After checking the results in freeview for this subject, I saw that the problem was that CA1 was including a big portion of white matter in its volume (see attached png). To try to solve the problem, I just reran the recon-all -hippo-subfield for the left hemisphere of this subject (which by the way did not solve the white matter inclusion). The problem I have now is that kvlQuantifyPosteriorProbabilityImages does not seem to "see" anymore the resulting volume on the left side and does not output any volume for the left side (see error below), although the output was properly created in the mri folder (i.e. all the posterior_left_* images are there and I can load them in freeview without any problem). Any guess? Many thanks for the help, Marie [maries-iMac:LONGITUDINAL_Stats/5272/mri] marie% kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_left_* volumeInVoxels: [maries-iMac:LONGITUDINAL_Stats/5272/mri] marie% kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_* volumeInVoxels: right_CA1: 3050.22 right_CA2-3: 8579.62 right_CA4-DG: 4997.83 right_fimbria: 354.868 right_hippocampal_fissure: 302.39 right_presubiculum: 3784.79 right_subiculum: 5384.07 [maries-iMac:LONGITUDINAL_Stats/5272/mri] marie% _______________________________________________ Freesurfer mailing list 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 dispose of the e-mail.
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