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 wrote:
External Email - Use CautionDear 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 wrote:
External Email - Use CautionDear 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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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