For question 1, try this
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
You did not say which MNI space you were dealing with (we use mni305, not 152).
On 7/15/2019 12:02 PM, Zhi Li wrote:
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Thank you very much, Tim. Any idea for the 1st question?
Thanks and best wishes,
Lizhi
On Sat, 13 Jul 2019 at 09:18, Tim Schäfer
<[email protected]<mailto:ts%[email protected]>> wrote:
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Dear Lizhi,
on your 2nd question: a rough explanation is on the FS Wiki at [1], but I found
this website [2] easier to follow as it has some example images.
Regarding space, I think they are all in native space. You can run `mri_info`
on them to get detailed information.
[1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
[2] http://www.grahamwideman.com/gw/brain/fs/fsunderstanding/fssampleimages.htm
Best,
Tim
> On July 12, 2019 at 9:30 PM Zhi Li
> <[email protected]<mailto:[email protected]>> wrote:
>
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> Now I have an annotation file in fsaverage space and a MNI voxel coordinate
> of one subject. May I ask how could I know if this coordinate is in one
> parcel of the annotation file? There are many coordinates that I cannot
> check it one by one in Freeview. In addition, if this is a native image
> coordinate how could I check whether it is in a parcel then?
>
> An additional question is whether the spaces of all the files in folder
> "mri" generated by recon-all are native individual space? What do the files
> 'orig.mgz', norm.mgz'', 'brainmask.mgz', 'brain.mgz' and 'T1.mgz' refer to?
> They are very similar to each other, with skull-stripped or not. Is there
> any document on it I could reference?
>
> Looking forward to your kind suggestions,
>
> Many thanks and best regards,
>
> Lizhi
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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