alveus (and fimbria) are defined to be part of the hippocampus in the
aseg. Did you include them in your calculation of subfield hippocampal
volume?
On Tue, 26 Feb 2013, Joshua Lee wrote:
I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus), perhaps this is not included in the
hipposubfields volumes?
Wondering, if I were to take a hand traced hippocampus rename it to aseg.mgz,
and made sure that the label matched what Freesurfer expects,
would the hipposubfields algorithm do its magic on this volume?
Joshua
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga <gariko...@gmail.com>
wrote:
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
Inline image 1
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias
<igles...@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
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> Freesurfer@nmr.mgh.harvard.edu
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--
-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@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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