<div dir="ltr">Thanks for the answer, <span style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">Denis</span>.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 24, 2014 at 6:22 PM, Denis-Alexander Engemann <span dir="ltr"><<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Peng, <div><br></div><div><br></div><div>one thing,<br><div class="gmail_extra"><br><br><div class="gmail_quote">
<div class="">On Mon, Mar 24, 2014 at 5:26 PM, peng <span dir="ltr"><<a href="mailto:prion.w@gmail.com" target="_blank">prion.w@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thank you Alex for the reply.<div>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:</div>
<div>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.</div>
<div>1.2 I cannot load -src.fif either in mne_analyze. It complains 'Come on, It is not an MEG/EEG measurement file'...</div><div><br></div><div>2. I tried the example in the script you provided (watershed), error happened while Decimating the dense tessellation...</div>
<p>"/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).</p>
</div></blockquote></div><div>that's part of the matlab command invoked. weird. is your Matlab path specified?</div><div>You can also use the python version `mne make_scalp_surfaces` which produces equivalent decimations.</div>
<span class="HOEnZb"><font color="#888888">
<div><br></div><div><br></div><div>Denis</div></font></span><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<p>3. If my data are MEG instead of EEG, do I still need to use this skin, skull, brain segmentations from watershed or <span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">mne_setup_source_space</span><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"> on brain surfaces is already sufficient?</span></p>
<p><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">Thank you very much and sorry about so many questions...</span></p><p><br></p></div><div><div><div class="gmail_extra">
<br><br><div class="gmail_quote">
On Fri, Mar 21, 2014 at 9:01 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-paristech.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
hi Peng,<br>
<div><br>
> I am new to MNE software. I wish to establish source space based on the<br>
> brain surface. I first run recon-all in freesurfer (latest version) to<br>
> generate potentially necessary files for MNE. Then I run<br>
> ===<br>
> mne_setup_source_space --subject <my subject> --ico 4 --overwrite<br>
> ===<br>
> to generate the source locations for a particular subject (<my subject>).<br>
><br>
> Then I had many files in the /bem folder, including an xxx-rh.pnt file,<br>
> which I assume is the coordinates of these locations in the right<br>
> hemisphere.<br>
<br>
</div>extension of source spaces is "-src.fif"<br>
<br>
a source space is defined relatively to a surface so it's not common<br>
to try to visualize it with freeview. I am not surprised you have coordinate<br>
alignment problems. But there is nothing to fix.<br>
<br>
basically you're good to go with the next step.<br>
<br>
For full script for the anatomical pipeline see for example:<br>
<br>
<a href="https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh" target="_blank">https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh</a><br>
<br>
HTH<br>
Alex<br>
<div><br>
<br>
<br>
> I then used freeview (part of freesurfer) to load the brain<br>
> image (/mri/brain.mgz) of this subject; and overlap xxx-rh.pnt as dot sets.<br>
> I surprisingly found these dots are not located one the surface of the white<br>
> matter as expected, but much lower (several centimeters).<br>
> If I changed <my subject> with fsaverage (template from freesurfer), and<br>
> re-run the above command, the new generated dots seemed to be on the correct<br>
> place.<br>
> Third, I changed <my subject> with an icbm152 asym template, the result was<br>
> similar to <my subject> : the dots were lower than the image.<br>
><br>
> So I am a little confused. Shall I do some coordinates transformation to<br>
> align these dots to the mri image? Or it is just a display problem of<br>
> freeview? I quickly browsed the manual and had not find a direct answer yet.<br>
> Thanks a lot for any hint!<br>
><br>
> best<br>
> Peng<br>
><br>
><br>
><br>
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