[Mne_analysis] MNE in Matlab

Sheraz Khan, PhD sheraz at nmr.mgh.harvard.edu
Thu Jan 18 10:05:55 EST 2018
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On the mne-python side you need to convert your data into Evoked object,
using mne python class
https://martinos.org/mne/dev/generated/mne.Evoked.html
And then you can use .save function exposed by Evoked object to save it
into -ave.fif file.

Please open issue on GitHub and share your pipeline with some sample data

Sheraz
> Thank you. I still got the error that the number of arguments was wrong.
> It
> seem to run adding just '1' for the argument "dSPM"). However, I get the
> following error:
>
> Error using fiff_read_evoked (line 83)
>
> Could not find processed data
>
>
>
> Error in mne_ex_compute_inverse (line 53)
>
> data = fiff_read_evoked(fname_data,setno);
>
>
> I noticed I have no -ave.fif file in the set of files computed with MNE
> python.
>
> Maybe that is the source of the issue?
>
>
> Ade
>
> On 18 January 2018 at 15:23, Sheraz Khan, PhD <sheraz at nmr.mgh.harvard.edu>
> wrote:
>
>> Some default values
>>
>> setno = 1; %(Event code that you put in your stimulus program)
>> nave = -1; %(Number of averages, -1 will read it from -ave.fif file)
>> dSPM = true; % (Convert the inverse map to Statistical score wrt to
>> baseline noise covirance)
>> lambda2 = 1/9 %(Default regularization parameter)
>>
>> HTH
>>
>> Sheraz
>>
>>
>> > Thank you, Sheraz.
>> >
>> > To assemble the inv operator I had a look at mne_ex_compute_inverse
>> and
>> > there are a number of arguments (e.g., setno [data set number],
>> lambda2,
>> > sDPM, sLORETA), that complicate things since I don't know where to get
>> > these values from or how to find them.
>> >
>> > Ade
>> >
>> > On 18 January 2018 at 14:20, Sheraz Khan, PhD <
>> sheraz at nmr.mgh.harvard.edu>
>> > wrote:
>> >
>> >> Hi Ade,
>> >>
>> >> > 1- Is the MNE Matlab toolbox a limited version of the python one? I
>> >> wonder
>> >> > if I can perform the whole pipeline (compute fwd and inv solutions)
>> >> with
>> >> > the Matlab version.
>> >>
>> >> MNE Matlab toolbox is mostly for IO, and was designed to complement
>> >> MNE-C
>> >> toolbox. It can not compute fwd and inv solutions.
>> >>
>> >>
>> >> > 2- If this is not possible, how to import in Matlab an already
>> >> computed
>> >> > inverse solution (oct-6-meg-inv.fif) into Matlab so I have the data
>> >> ready
>> >> > for further analysis in Matlab?
>> >>
>> >> You can use mne_read_inverse_operator.m function to read inv operator
>> >> into
>> >> Matlab, but you need to assemble it. Please see
>> mne_ex_compute_inverse.m
>> >> for example.
>> >>
>> >> HTH
>> >>
>> >> Best
>> >>
>> >> Sheraz
>> >>
>> >>
>> >> > Hi everyone,
>> >> >
>> >> > Two questions:
>> >> >
>> >> > 1- Is the MNE Matlab toolbox a limited version of the python one? I
>> >> wonder
>> >> > if I can perform the whole pipeline (compute fwd and inv solutions)
>> >> with
>> >> > the Matlab version.
>> >> > 2- If this is not possible, how to import in Matlab an already
>> >> computed
>> >> > inverse solution (oct-6-meg-inv.fif) into Matlab so I have the data
>> >> ready
>> >> > for further analysis in Matlab?
>> >> >
>> >> > Thank you,
>> >> > Ade
>> >> > _______________________________________________
>> >> > Mne_analysis mailing list
>> >> > Mne_analysis at nmr.mgh.harvard.edu
>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>
>> >>
>> >> -------------------------
>> >> 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
>> >> _______________________________________________
>> >> Mne_analysis mailing list
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>> >>
>> >>
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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


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