Thanks Juan Eugenio, we have visually inspected the segmentations, and we observe that the volume differences between aseg and hippo-subfields are constants among subjects, and consistent in both left and right hemispheres (please see table attached, columns diff.aseg.left.subfields and diff.aseg.right.subfields). Indeed, the percentage of the difference between the aseg and the hippo-subfields is about 20% average (19.5% for the left and 22.1% for the right hemisphere), and there are not strong differences at the individual subject level.
The aseg values always are bigger than the hippo-subfields across all planes (please see attached photos with some examples). And, as it can be seen in the attached pictures, the hippo-subfield segmentation seems to be more accurate than the aseg one.
We used the standard recon-all procedure with -hippo-subfields -qcache -all
Considering that these differences are pretty consistent across subjects, Do you think that there is anything wrong with our results? Or anything that we are missing in our analysis?
Thank you very much, Gari
[image: Inline image 1]
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote:
Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure.
I obtain quite different values, for example:
row.names lh.aseg lhHIP rh.aseg rhHIP 1 S_00 4848.8 3828.187 4878.8 3767.739 2 S_02 4153.8 3371.517 4547.6 3389.918
Am I doing anything wrong? Should I calculate the hippos subfields volumes differently?
Many thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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