[Mne_analysis] Alarmingly similar results for subcortical source activity

[Alan]

Hi Junpeng,

Yes, the function mne.source_space.get_segment_positions in on my current
development branch.

https://github.com/leggitta/mne-python/tree/gsoc-subcortical

I modified the file /mne/source_space.py to include this additional
function.

I think you can checkout my development branch and then you should be able
to run /mne/examples/inverse/plot_subcortical_activation.py to get the same
results.

Cheers,
Alan


On Tue, Jun 3, 2014 at 3:15 PM, junpeng.zhang <junpeng.zhang at gmail.com>
wrote:

> Hi Alan,
> Thank you for your contribution to the field.
> My simple question is,
> amyg_pos = mne.source_space.get_segment_positions('spm', 'Right-Amygdala',
>
>                    subjects_dir=subjects_dir)
>
> In the above code, the function  mne.source_space.get_segment_positions is
> written by you?
> How to understand the function get_segment_positions? Where to find the
> defination and explanation of mne.source_space and get_segment_positions?
> Could I run the .py in my computer and could I get your results?
> Best wishes, and thank you for your contribution.
> Junpeng Zhang
>
>
>
>
> 发件人：Alan <leggitta3 at gmail.com>
> 发送时间：2014-06-03 08:13
> 主题：[Mne_analysis] Alarmingly similar results for subcortical source
> activity
> 收件人："mne_analysis at nmr.mgh.harvard.edu"<mne_analysis at nmr.mgh.harvard.edu>
> 抄送：
>
> Hello,
>
>
> I've been looking at right amygdala activity in the spm faces dataset as a
> means of developing subcortical source localization tools. I've tried two
> different methods so far.
>
> 1.) I did a whole brain volume analysis (dSPM) and then averaged together
> vertices belonging to the right amygdala (code here).
>
> 2.) I merged the left and right cortical surface source spaces with a
> right amygdala volume source space, performed dSPM and then averaged
> together the volume sources (code here).
>
> I've attached the evoked plots for each condition (grey bars indicate
> regions of significant difference using independent t-tests per time point
> with fdr correction).
>
>
> The results of each method are so similar that I'm concerned they may be
> derived from a common source of error. Can anyone think of think of any
> probable sources of error and suggest other ways to validate these methods?
> I haven't yet ventured into simulated data, but I think that's going to be
> the next step.
>
> Thanks!
> Alan
>
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