[Mne_analysis] MEG-MRI coordinate system alignment

Vincent Rupp Jr. vincentruppjr at gmail.com
Tue Jun 4 13:45:16 EDT 2013
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Thanks very much for the help. Great info.

Best wishes,

Vincent Rupp Jr


On Mon, Jun 3, 2013 at 6:13 AM, Alexandre Gramfort <
gramfort at nmr.mgh.harvard.edu> wrote:

> hi Vincent,
>
> if you look in:
>
>
> https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh
>
> you'll read:
>
> # Make high resolution head surface
> mkheadsurf -s ${SUBJECT}
> mne_surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --id 4
> --check --fif ${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif
> # if the previous command fails you can use the --force option.
>
> if this step succeeds you'll have a high resolution scalp for
> coregistration rather than the BEM surface.
>
> HTH
> Alex
>
>
> On Mon, Jun 3, 2013 at 1:37 PM, Hari Bharadwaj <hari at nmr.mgh.harvard.edu>
> wrote:
> > Hi,
> >    It uses whatever "subject-head.fif" surface lives in the Freesurfer
> > $SUBJECTS_DIR/$SUBJECT/bem/ directory. This is usually prepared by
> > mne_watershed_bem unless you created this using mne_surf2bem from
> > something else.
> >
> > Also, the answer to your latter question depends on why you replaced the
> > surfaces from mne_watershed_bem...Assuming your previous registrations
> > were with a reasonable head surface, since the number of parameters for
> > the MEG head to MRI head transformation is small compared to the number
> of
> > digitizer points, I'd say it is not necessary to re-register.
> >
> > HTH,
> > Regards,
> > Hari
> >
> > On Sun, June 2, 2013 7:31 pm, Vincent Rupp Jr. wrote:
> >> Hi,
> >>
> >> According to the
> >> manual<
> http://martinos.org/mne/manual/analyze.html#coordinate-frame-alignment>,
> >> the MRI-MEG coordinate frame alignment tools included in mne_analyze
> >> utilize the 3D digitizer (Polhemus) data acquired in the beginning of
> each
> >> MEG/EEG session and the scalp surface triangulation. Specifically what
> >> scalp surface triangulation is used here? Is this something generated
> >> during FreeSurfer's recon-all stream, or is it the BEM mesh created with
> >> mne_watershed_bem?
> >>
> >> Ultimately, I am trying to understand how to solve this question: I
> >> recently overwrote my output from mne_setup_source_space,
> >> mne_watershed_bem, and mne_setup_forward_model. Do I need to re-register
> >> my
> >> MEG/MRI data before proceeding to compute the forward solution?
> >>
> >>
> >> Best wishes,
> >>
> >> Vincent Rupp Jr
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > --
> > Hari Bharadwaj
> > PhD Candidate, Biomedical Engineering,
> > Boston University
> > 677 Beacon St.,
> > Boston, MA 02215
> >
> > Martinos Center for Biomedical Imaging,
> > Massachusetts General Hospital
> > 149 Thirteenth Street,
> > Charlestown, MA 02129
> >
> > hari at nmr.mgh.harvard.edu
> > Ph: 734-883-5954
> >
> >
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