[Mne_analysis] extract label time course for resting state data

[Sheraz Khan, PhD]

Its on GitHub but in private repository :-)

I can email you the relevant sections.

Thanks

Sheraz


> Great! Thanks!
>
> Using the code in the previous email I've extracted the time course of the
> Lausanne125 parcellation. I just need to double check it.
>
> Is your code on the mne-hcp github?
>
>
> Thanks,
>
> Noam
>
> ________________________________
> From: Sheraz Khan, PhD <sheraz at nmr.mgh.harvard.edu>
> Sent: Friday, October 20, 2017 6:21:41 PM
> To: Discussion and support forum for the users of MNE Software
> Cc: Discussion and support forum for the users of MNE Software; Peled,
> Noam
> Subject: Re: [Mne_analysis] extract label time course for resting state
> data
>
> Hi Noam,
>
> Denis and me, work a lot on label representative time series, I have some
> adhoc code you might try.
>
> Thanks
>
> Sheraz
>
>
>> Hi Noam,
>>
>> I think you might want to use the utils we engineered with Sheraz
>> earlier
>> this year. I will contribute them to MNE over the forthcoming months.
>> But
>> the API might change a bit as not everyone agrees that we should use
>> mne.io.RawArray as terminal container for source rest time courses.
>>
>> Denis
>> On Fri 20 Oct 2017 at 22:46, Peled, Noam <NPELED at mgh.harvard.edu> wrote:
>>
>>> I ended up using the following code, instead of
>>> stc.extract_label_time_course:
>>>
>>> label_flip = mne.label_sign_flip(label, src)[:, None].squeeze()
>>> label_flip = np.tile(label_flip, (stc.data.shape[1], 1)).T
>>> label_tc = np.mean(label_flip * stc.data, axis=0)
>>>
>>>
>>> The problem was in the last line. originally it's:
>>>
>>> np.mean(flip * stc.data[vertidx, :], axis=0)
>>> Which doesn't work if the stc was calculated specifically for the label
>>> using
>>>
>>> mne.minimum_norm.apply_inverse_raw(
>>>     raw, inverse_operator, lambda2, inverse_method, label=label)
>>>
>>>
>>> Does it make sense?
>>> Thanks,
>>>
>>> Noam
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------
>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
>>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Peled, Noam <
>>> NPELED at mgh.harvard.edu>
>>> *Sent:* Friday, October 20, 2017 4:10:46 PM
>>> *To:* mne_analysis at nmr.mgh.harvard.edu
>>> *Subject:* [Mne_analysis] extract label time course for resting state
>>> data
>>>
>>>
>>> Hi all,
>>>
>>> I'm trying to extract the labels time course for a long resting state
>>> data
>>> (from HCP)
>>>
>>> What would be a good approach for that?
>>>
>>> I've tried first to use mne.minimum_norm.apply_inverse_raw, but it was
>>> too much for my computer and it crashed because of memory error.
>>>
>>> Then, I've tried to create an stc file for each label, to extract later
>>> the time course. But then I got the error that the stc is not
>>> compatible
>>> with source space, which it true.
>>>
>>> Maybe I should use the apply_inverse_raw each time for short windows? I
>>> prefer to get the full time course of each label if possible.
>>>
>>>
>>> Thanks,
>>>
>>> Noam
>>>
>>>
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>
>
> -------------------------
> Sheraz Khan, M.Eng, Ph.D.
> Instructor in Neurology
>
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Harvard Medical School
>
> McGovern Institute for Brain Research
> Massachusetts Institute of Technology
>
> Tel:   +1 617-643-5634
> Fax:   +1 617-948-5966
> Email: sheraz at nmr.mgh.harvard.edu
>        sheraz at mit.edu
> Web:   http://sheraz.mit.edu
>


-------------------------
Sheraz Khan, M.Eng, Ph.D.
Instructor in Neurology

Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School

McGovern Institute for Brain Research
Massachusetts Institute of Technology

Tel:   +1 617-643-5634
Fax:   +1 617-948-5966
Email: sheraz at nmr.mgh.harvard.edu
       sheraz at mit.edu
Web:   http://sheraz.mit.edu