External Email - Use Caution Dear all,
Thank you very much for your kind suggestions. I think it should be mni305. I know how to deal with it now. According to my understanding, the label files transformed from annotations file in the fsaverage should be the mni305 atlas. Then I could get the coordinate of each vertex in each label through read_labels. Thanks again. Best wishes, Lizhi On Tue, 16 Jul 2019 at 04:03, Tim Schäfer <ts...@rcmd.org> wrote: > External Email - Use Caution > > 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." < > dgr...@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...@rcmd.org<mailto: > ts%2...@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.ps...@gmail.com<mailto: > lizhi.ps...@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 > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu<mailto: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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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