[Mne_analysis] a junior question on mne_setup_source_space

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Fri Mar 21 16:01:41 EDT 2014
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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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