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I did something similar once. There is a paper on MNI152 to fsaverage conversion options (that suggests a pretty accurate, new method) here: https://www.ncbi.nlm.nih.gov/pubmed/29770530/

If I remember correctly, the simplest way, even though it's not terribly accurate, is to use the information on the website that Douglas linked to go from MNI152 to MNI305, then check for the label of the closest fsaverage vertex in the annot.

Best,

Tim

> On July 16, 2019 at 4:57 AM "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> wrote:
>
>
> 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:
>
>         External Email - Use Caution
>
> 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 <ts+ml@rcmd.org<mailto:ts%2Bml@rcmd.org>> wrote:
>         External Email - Use Caution
>
> 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 <lizhi.psych@gmail.com<mailto:lizhi.psych@gmail.com>> 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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--
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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