[Mne_analysis] a junior question on mne_setup_source_space

Mon Mar 24 13:22:12 EDT 2014

Hi Peng,

one thing,

On Mon, Mar 24, 2014 at 5:26 PM, peng <prion.w at gmail.com> wrote:

> 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).
>
that's part of the matlab command invoked. weird. is your Matlab path
specified?
You can also use the python version `mne make_scalp_surfaces` which
produces equivalent decimations.

Denis

> 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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