[Mne_analysis] Dicom organization

Denis-Alexander Engemann denis.engemann at gmail.com
Mon Aug 4 17:35:20 EDT 2014
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Isahiah,

if you prefer Matlab you can also use `mne_make_scalp_surfaces` which is a
shell script that calls Matlab and is provided by MNE-C.



On Mon, Aug 4, 2014 at 11:30 PM, Isaiah C. Smith <
Isaiah.C.Smith.17 at dartmouth.edu> wrote:

> Thanks so much for the help but sorry,
> I looked at the Python, but I am not really familiar with the format and
> having a hard time determining how to implement it. The lab I am working in
> primarily uses MATLAB. Is there a way to form models in MATLAB or the
> terminal along the same lines as the python attachment? And does the
> creation of a brain model follow the same procedures as the scalp and skull?


All is absed on your freesurfer segmentation, in that regard things are
similar. The brain model (source space + forward solution) of course are
not generated the same way as the head model.
Hope these vague remarks help ...


> Isaiah
> On Aug 4, 2014, at 2:11 PM, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
>
> >> # Make high resolution head surface
> >> HEAD_FNAME=${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif
> >> if [ ! -f ${HEAD_FNAME} ];
> >> then
> >>    mkheadsurf -s ${SUBJECT}
> >>    mne_surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --id 4
> >> --check --fif ${HEAD_FNAME}
> >> fi
> >>
> >> # Setup BEM
> >>
> >> to create the head surface. Or do I have to create the boundaries?
> >
> > this sets up the head surface for coregistration with mne_analyze.
> > It will not be used for forward modeling but just to create the
> -trans.fif file.
> >
> > Try what denis suggests if this does not succeed for you.
> >
> > Alex
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