2017-07-25 20:51 GMT+03:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:

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.
>
> Now I try to match the coordinates, according to the linked you posted.
> The brain space in results is of 256x256x256 voxels. What are the
> dimensions of each voxel here?
> If I need to compare that results to another analysis that come from
> SPM, so case #2 is the way? And then, I'll need in fact the
> coordinates from mri_cor2label?
>
> Thanks for the fast and useful replies.
> Adiel
>
> 2017-07-24 22:11 GMT+03:00 Douglas Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>:
>
> 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 here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems>
>
> using case #2
>
>
> On 7/24/17 2:11 AM, 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
>> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>:

>>
>> 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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