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%



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