<div dir="ltr"><br><div class="gmail_extra">Thank you alex.<br><br><div class="gmail_quote">On Mon, Mar 24, 2014 at 6:38 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 class=""><br>
> Thank you Alex for the reply.<br>
> 1. I suppose you meant freeview is not the optimal tool for visualizing<br>
> source space of mne. However, I wish to check the source space by<br>
> visualisation before I move on to source reconstructions. I tried<br>
> mne_analyze instead of freeview:<br>
<br>
</div>a source space contains the indices of the vertices used in the surface<br>
segmented by freesurfer.<br></blockquote><div>I misunderstood it before, I thought it contained were 3-D coordinates. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
See fig on the right in:<br>
<br>
<a href="http://www.frontiersin.org/files/Articles/70133/fnins-07-00267-r2/image_m/fnins-07-00267-g003.jpg" target="_blank">http://www.frontiersin.org/files/Articles/70133/fnins-07-00267-r2/image_m/fnins-07-00267-g003.jpg</a><br>
<br>
in the recent paper on MNE-Python:<br>
<br>
<a href="http://journal.frontiersin.org/Journal/10.3389/fnins.2013.00267/full" target="_blank">http://journal.frontiersin.org/Journal/10.3389/fnins.2013.00267/full</a><br>
<br>
so if you want to check the source space I guess you want to check the<br>
freesurfer segmentation.<br>
<div class=""><br></div></blockquote><div>I will try. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">
> 1.1 It seemed to detect surfaces generated by freesurfer (such as inflated<br>
> etc.) automatically, which I can load by <load surfaces...> in the menu; but<br>
> not those surfaces generated by watershed, even after I copy them to the<br>
> <surf> subfolder under the subject folder.<br>
<br>
</div>watershed is for the BEM not the source space.<br>
you should be able to view them with freeview though.<br>
<div class=""><br>
> 1.2 I cannot load -src.fif either in mne_analyze. It complains 'Come on, It<br>
> is not an MEG/EEG measurement file'...<br>
<br>
</div>yes it's not really meant to be visualized. I can send you script used<br>
to make the figure on the frontiers paper if you want.<br></blockquote><div>Thanks, it will help. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class=""><br>
> 2. I tried the example in the script you provided (watershed), error<br>
> happened while Decimating the dense tessellation...<br>
><br>
> "/Applications/MNE-2.7.4-3378-MacOSX-x86_64/bin/mne_make_scalp_surfaces:<br>
> line 125: -nojvm: command not found". I do have <mne_make_scalp_surfaces><br>
> file in the path. (Platform: MacOS10.9.2, macbook pro).<br>
<br>
</div>it's because mne_make_scalp_surfaces used matlab for decimation.<br>
there is a python alternative. </blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Try<br>
<br>
mne make_scalp_surfaces<br>
<br>
if you have mne python installed correctly.<br>
<br>
but it's just for visualization not computation.<br></blockquote><div>OK, I will double check my Matlab routes and try Python if it still doesn't work. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class=""><br>
> 3. If my data are MEG instead of EEG, do I still need to use this skin,<br>
> skull, brain segmentations from watershed or mne_setup_source_space on brain<br>
> surfaces is already sufficient?<br>
<br>
</div>you need the inner skull. This command should do the job:<br>
<br>
mne_setup_forward_model --homog --surf --ico 4<br></blockquote><div> </div><div>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?</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
then mne_do_forward_solution<br>
<br>
see :<br>
<br>
<a href="https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_tutorial.sh" target="_blank">https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_tutorial.sh</a><br>
<br>
for a full script.<br>
<br>
maybe:<br>
<br>
<a href="http://martinos.org/mne/dev/command_line_tutorial.html#command-line-tutorial" target="_blank">http://martinos.org/mne/dev/command_line_tutorial.html#command-line-tutorial</a><br>
<br>
this can help too although it's not really up to date (but it should work)<br>
<div class=""><br>
</div></blockquote><div>Great, I will try them then. many thanks again. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">> Thank you very much and sorry about so many questions...<br>
<br>
</div>no pb<br>
<br>
Alex<br>
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