finding coordinates is the same problem as putting the results into the
same space (except probably harder). There is not a simple formula for
converting one to the other. Eg, fsaverage uses MNI305 space. What is
SPM using? You have to figure out all these things to convert
On 07/26/2017 04:10
Oh, sure you are right.
But each analysis is done on different protocols, and also, for now I
already have many of analysis results that has been run on the SPM and on
Freesurfer, and has a difference in coordinates.
So- for now, what is the right way to treat that? the link that you gave up
here?
I would put the spm and fs analysis into the same space
On 07/25/2017 10:19 AM, עדיאל חרבש wrote:
> Hi Douglas,
> Thank you, works perfectly.
> But, I need to know first which structures id's are inside each file.
> I preferred to extract all the brain map with Matlab, as Bruce commented.
>
> No
Hi Douglas,
Thank you, works perfectly.
But, I need to know first which structures id's are inside each file. I
preferred to extract all the brain map with Matlab, as Bruce commented.
Now I try to match the coordinates, according to the linked you posted.
The brain space in results is of 256x256x2
Hi Bruce,
I had Matlab and freesurfer on separate machines.
But for now I managed to have Matlab on both, so I can run it.
It really helped, thanks!
Adiel
2017-07-24 22:33 GMT+03:00 Bruce Fischl :
> HI Adiel
>
> we distribute all our matlab scripts as part of FreeSurfer
>
>
> cheers
> Bruce
> On
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_ext
If you want all the coordinates for a given segment (eg, left hippo),
then you can run mri_cor2label --i aparc+aseg.mgz --id 17 --l file.label
17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt
The coordinates will be in "tkregister space" which you can convert to
MNI305 using the info from
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 :
> Hi Adiel
>
> in matlab you could do something
Hi Adiel
in matlab you could do something like:
cd $SUBJECTS_DIR//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 u
ubject: Re: [Freesurfer] help with finding exact and detailed coordinates
of brain areas
To: Freesurfer support list
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 t
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 specificit
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
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
som
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