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

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 <fischl@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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