Hi Aya,
you can convert the aseg back to the original voxel space with
mri_convert. I think the cmdline would be:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz
-rl = reslice like
-rt = resample type
cheers
Bruce
On Wed, 27 Oct 2010,
Aya Ben
Yakov wrote:
Hi
I'm sorry for all these questions, but I'm very new to freesurfer, and I still
don't really understand how things work.
Is it necessary to convert to nifti? if I understand correctly, mri.vol should
hold the needed information. In what space is this information
(assuming some processing was done on the original data)?
Can I convert it back to the original data space? or to talairach?
The original data includes only 256X256X176, since there were only 176 slices,
yet in mri.vol there are 256 slices.
In short - how can I convert correctly to the original space and to talairach?
Thanks for your help!
Aya
__________________________________________________
From Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Sent Wed 10/27/2010 2:41 PM
To Ørjan Bergmann <orjan.bergm...@medisin.uio.no>
Cc freesurfer@nmr.mgh.harvard.edu
Subject Re: [Freesurfer] subcortical structure coordinates
yes, and all the volumes have the same index structure, so you can load
any of them. The aseg.mgz contains the labeled volume, with the label to
structure name conversion in the FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote:
I'm also interested in these segmentations for analysis in Matlab.
In particular, which volumes should be loaded to get the coordinates of the
segmentations?
I assume the segmentation volumes are just indices (all voxel belonging to
the same segment are assigned the same unique index), correct ?
---
Sincerly,
Dr. Ørjan Bergmann
On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fis...@nmr.mgh.harvard.edu
(mailto:fis...@nmr.mgh.harvard.edu)>wrote:
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume
Brainvoyager can read. You can load any of our volumes into matlab with
either MRIread.m or load_mgh.m and go from there.
cheers
Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I
would now like to transfer the data to Matlab. I am looking for a way to
load the coordinates of all structures (or, if it isn't possible, for each
structure, by its number) to Matlab, in Talairach coordinates. Is this
possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow
use the segmentation from FreeSurfer for analysis in Matlab, in combination
with data I have from BrainVoyager (the functional data). I don't
necessarily need talairach coordinates, but otherwise I'm not sure how it
would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions?
Thanks!
Aya
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