Dear Freesurfer Developers and Users,
I have two question(s) about Freesurfer and individual subject's MNI coordinates:
(1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer.
(2) Once I have obtained (in matlab), for a list of voxels that comprise the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile?
I searched the archives but could not find information that explained this directly; apologies if this does already exist: if so, could you please point me towards it?
Thank you so much for your help,
Best wishes, Nela
---- Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford
Tel: 01865 282274 Internal: 82274
1. Yes, just apply the talairach.xfm transform to each vertex. Should be easy enough to do in matlab using read_surf.m.
2. Yes, this can also be done in matlab, saving either in "curv" (write_curv.m) or wfile format.
On Sat, 22 Oct 2011, Nela Cicmil wrote:
Dear Freesurfer Developers and Users,
I have two question(s) about Freesurfer and individual subject's MNI coordinates:
(1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer.
(2) Once I have obtained (in matlab), for a list of voxels that comprise
the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile?
I searched the archives but could not find information that explained
this directly; apologies if this does already exist: if so, could you please point me towards it?
Thank you so much for your help,
Best wishes, Nela
Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford
Tel: 01865 282274 Internal: 82274 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
For #1, it might be easier to use mri_surf2surf with the --sval-tal-xyz option. See the --help for more info. doug
Bruce Fischl wrote:
- Yes, just apply the talairach.xfm transform to each vertex. Should be
easy enough to do in matlab using read_surf.m.
- Yes, this can also be done in matlab, saving either in "curv"
(write_curv.m) or wfile format.
On Sat, 22 Oct 2011, Nela Cicmil wrote:
Dear Freesurfer Developers and Users,
I have two question(s) about Freesurfer and individual subject's MNI coordinates:
(1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer.
(2) Once I have obtained (in matlab), for a list of voxels that comprise
the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile?
I searched the archives but could not find information that explained
this directly; apologies if this does already exist: if so, could you please point me towards it?
Thank you so much for your help,
Best wishes, Nela
Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford
Tel: 01865 282274 Internal: 82274 _______________________________________________ Freesurfer mailing list 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Nela Cicmil