[Mne_analysis] a junior question on mne_setup_source_space

[peng]

Thank you Alex for the reply.
1. I suppose you meant freeview is not the optimal tool for visualizing
source space of mne. However, I wish to check the source space by
visualisation before I move on to source reconstructions. I tried
mne_analyze instead of freeview:
1.1 It seemed to detect surfaces generated by freesurfer (such as inflated
etc.) automatically, which I can load by <load surfaces...> in the menu;
but not those surfaces generated by watershed, even after I copy them to
the <surf> subfolder under the subject folder.
1.2 I cannot load -src.fif either in mne_analyze. It complains 'Come on, It
is not an MEG/EEG measurement file'...

2. I tried the example in the script you provided (watershed), error
happened while Decimating the dense tessellation...

"/Applications/MNE-2.7.4-3378-MacOSX-x86_64/bin/mne_make_scalp_surfaces:
line 125: -nojvm: command not found". I do have <mne_make_scalp_surfaces>
file in the path. (Platform: MacOS10.9.2, macbook pro).

3. If my data are MEG instead of EEG, do I still need to use this skin,
skull, brain segmentations from watershed or mne_setup_source_space on
brain surfaces is already sufficient?

Thank you very much and sorry about so many questions...




On Fri, Mar 21, 2014 at 9:01 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> hi Peng,
>
> >  I am new to MNE software. I wish to establish source space based on the
> > brain surface. I first run recon-all in freesurfer (latest version) to
> > generate potentially necessary files for MNE. Then I run
> > ===
> > mne_setup_source_space --subject <my subject> --ico 4 --overwrite
> > ===
> > to generate the source locations for a particular subject (<my subject>).
> >
> > Then I had many files in the /bem folder, including an xxx-rh.pnt file,
> > which I assume is the coordinates of these locations in the right
> > hemisphere.
>
> extension of source spaces is "-src.fif"
>
> a source space is defined relatively to a surface so it's not common
> to try to visualize it with freeview. I am not surprised you have
> coordinate
> alignment problems. But there is nothing to fix.
>
> basically you're good to go with the next step.
>
> For full script for the anatomical pipeline see for example:
>
>
> https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh
>
> HTH
> Alex
>
>
>
> > I then used freeview (part of freesurfer) to load the brain
> > image (/mri/brain.mgz) of this subject; and overlap xxx-rh.pnt as dot
> sets.
> > I surprisingly found these dots are not located one the surface of the
> white
> > matter as expected, but much lower (several centimeters).
> > If I changed <my subject> with fsaverage (template from freesurfer), and
> > re-run the above command, the new generated dots seemed to be on the
> correct
> > place.
> > Third, I changed <my subject> with an icbm152 asym template, the result
> was
> > similar to <my subject> : the dots were lower than the image.
> >
> > So I am a little confused. Shall I do some coordinates transformation to
> > align these dots to the mri image? Or it is just a display problem of
> > freeview? I quickly browsed the manual and had not find a direct answer
> yet.
> > Thanks a lot for any hint!
> >
> > best
> > Peng
> >
> >
> >
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