HI Adiel
we distribute all our matlab scripts as part of FreeSurfer
cheers
Bruce
On Mon, 24 Jul
2017, עדיאל חרבש wrote:
Hi Bruce,
It may really help to shorten and ease the procedure, thanks.
I see that I should clone all your matlab repository to use this function?
I will look over mri_extract_labels as well.
Best,
Adiel
2017-07-24 17:02 GMT+03:00 Bruce Fischl <[email protected]>:
Hi Adiel
in matlab you could do something like:
cd $SUBJECTS_DIR/<subject id>/mri
matlab
[v,M,mr] = load_mgh('aseg.mgz');
left_hippo_indices = find(v == 17);
where the '17' comes from
$FREESURFER_HOME/FreeSurferColorLUT.txt and is the index for
left hippocampus.
Is that would you mean? Or you could use mri_extract_labels to
build volumes that have only the labels you want in them.
cheers
Bruce
On Mon, 24 Jul 2017, עדיאל חרבש wrote:
Hi Bruce,
Thanks for the reply.
By "coordinates" I mean all the voxels that belong
to a certain structure. I
think it's called "labels"? I interest in the main
structures like
Hippocampus, Thalamus, Cerebellum, Amygdala, corpus
callosum, etc. If the
standard segmentation segments in that specificity
only the lobes, it can be
good enough...
I see the .mgz files, but can not extract them...
How should I do that?
Thank for the patience..
Adiel
2017-07-23 18:09 GMT+03:00 Bruce Fischl
<[email protected]>:
Hi Adiel
what kind of coordinates do you mean, and
which brain structures
are you interested in? Our standard
segmentation is sampled into
the volume in files named aparc*+aseg.mgz, but
the Brodmann area
estimates are on the surface.
cheers
Bruce
On Sun, 23 Jul 2017, עדיאל חרבש wrote:
Hi,
I'm very new to Freesurfer, and actually
work with
some exist results of
other people. The results are from the
call of
"-recon all -autorun".
I try to get all the coordinates of each
of the
structures of the brain,
that segmented. I can find on files only
the volumes
of some structures and
something that look like detailed
coordinates of
Brodman Areas only. But I
can't find the detailed coordinates of
all
structures in brain.
I'll be grateful if someone can guide me
where can I
find it, or what should
I do to get these results.
Thanks,
Adiel
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