[Mne_analysis] a junior question on mne_setup_source_space

[peng]

Thanks for the answer, Denis.


On Mon, Mar 24, 2014 at 6:22 PM, Denis-Alexander Engemann <
denis.engemann at gmail.com> wrote:

> 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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>>
>>
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