[Mne_analysis] MEG-MRI coordinate system alignment

[Alexandre Gramfort]

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
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>