sure. Good luck
Bruce
On Sun, 3 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce and Josh, the sum of all the hippo-subfields included
all (the fimbria as well) except the fissure. We don't have
hippo-subfields values related to the alveus (we run the standard command
-hippo-subfields -all).
As suggested by Eugenio and Koen, we are going to use the -hippo-subfields
values as we need the subfields volumes as well.
many thanks for your answers!
Gari
On Tue, Feb 26, 2013 at 11:34 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
---------------------------------------------------------------------------
----------
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
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