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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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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 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.orgmailto: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.commailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 CautionThank 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.orgmailto: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.commailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
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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+ml@rcmd.org wrote:
External Email - Use CautionI 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 CautionThank 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 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<mailto:
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Tim Schäfer -
Zhi Li