[Mne_analysis] a junior question on mne_setup_source_space

peng prion.w at gmail.com
Tue Mar 25 03:29:08 EDT 2014
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Thank you alex.

On Mon, Mar 24, 2014 at 6:38 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> hi 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:
>
> a source space contains the indices of the vertices used in the surface
> segmented by freesurfer.
>
I misunderstood it before, I thought it contained were 3-D coordinates.

>
> See fig on the right in:
>
>
> http://www.frontiersin.org/files/Articles/70133/fnins-07-00267-r2/image_m/fnins-07-00267-g003.jpg
>
> in the recent paper on MNE-Python:
>
> http://journal.frontiersin.org/Journal/10.3389/fnins.2013.00267/full
>
> so if you want to check the source space I guess you want to check the
> freesurfer segmentation.
>
> I will try.

> > 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.
>
> watershed is for the BEM not the source space.
> you should be able to view them with freeview though.
>
> > 1.2 I cannot load -src.fif either in mne_analyze. It complains 'Come on,
> It
> > is not an MEG/EEG measurement file'...
>
> yes it's not really meant to be visualized. I can send you script used
> to make the figure on the frontiers paper if you want.
>
Thanks, it will help.

>
> > 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).
>
> it's because mne_make_scalp_surfaces used matlab for decimation.
> there is a python alternative.


>
Try
>
> mne make_scalp_surfaces
>
> if you have mne python installed correctly.
>
> but it's just for visualization not computation.
>
OK, I will double check my Matlab routes and try Python if it still doesn't
work.

>
> > 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?
>
> you need the inner skull. This command should do the job:
>
> mne_setup_forward_model --homog --surf --ico 4
>

Does that mean I will set my source space on inner skull? Would you think
it better on the surface of white matter better or practically no much
difference?

>
> then mne_do_forward_solution
>
> see :
>
>
> https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_tutorial.sh
>
> for a full script.
>
> maybe:
>
>
> http://martinos.org/mne/dev/command_line_tutorial.html#command-line-tutorial
>
> this can help too although it's not really up to date (but it should work)
>
> Great, I will try them then. many thanks again.


> > Thank you very much and sorry about so many questions...
>
> no pb
>
> Alex
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