[Mne_analysis] MNE in Matlab

Adela Glez. adelaglezcom at gmail.com
Tue Jan 23 18:00:00 EST 2018
Search archives: 
Thanks again, Sheraz.

I am confused because my original question was how to compute the source
data (in Matlab) if I already have the inverse solution. You mentioned I
could use mne_read_inverse_operator.m but I should assemble it and referred
me to the function mne_ex_compute_inverse.m. But this function asks for the
_ave-fif file, which I don't have, and seems to me that it is rather to
compute the inverse solution, which I already have ("% An example on how to
compute a L2-norm inverse solution, and not to create the source estimates.

I had a look at how the source data is computed in Python and it just uses
"read_inverse_operator" to read the inv solution, and "apply_inverse_raw"
for the source estimation (which is what I aim to do in Matlab), which
doesn't need the _ave.fif file.

Maybe I am misunderstanding something?
Thank you,
Ade


On 18 January 2018 at 17:05, Sheraz Khan, PhD <sheraz at nmr.mgh.harvard.edu>
wrote:

> 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
> >> >> Mne_analysis at nmr.mgh.harvard.edu
> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >>
> >> >>
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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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