[Mne_analysis] MNE in Matlab

Adela Glez. adelaglezcom at gmail.com
Fri Jan 26 16:27:24 EST 2018
Search archives: 
Thank you! This is great. I will have a look soon.


On 25 January 2018 at 03:07, Sheraz Khan, PhD <sheraz at nmr.mgh.harvard.edu>
wrote:

> Please find gist at
>
> https://gist.github.com/SherazKhan/866dd62722b46a39ec6f8ce3f1806a68
>
>
> fname_inv = 'sample_audvis-meg-oct-6-meg-fixed-inv.fif'
> fname_raw = 'sample_audvis_tsss.fif'
> sol = apply_inverse_raw(fname_raw,fname_inv)
>
>
> As you can see, it is done using mne-matlab function.
>
> The wisdom behind not assembling inverse operator in the inverse file, is
> to make it general, so that same inverse operator can be applied to raw or
> ave file.
>
> HTH
>
> Best
>
> Sheraz
>
>
>
>
> > Thank you very much, Sheraz, you are very kind to do so.
> > So is there at the moment no way to do this in Matlab as per the Matlab
> > set
> > of functions provided by MNE?
> > Ade
> >
> > On 24 January 2018 at 05:35, Sheraz Khan, PhD <
> sheraz at nmr.mgh.harvard.edu>
> > wrote:
> >
> >> Hi Adela,
> >>
> >> You can do the same in Matlab, Tomorrow, I will create a small matlab
> >> gist
> >> for you, in which, you input raw and inv file, and it outputs source
> >> estimates, like apply_inverse_raw in mne-python.
> >>
> >> Best
> >>
> >> Sheraz
> >>
> >> > 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
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> The information in this e-mail is intended only for the person
> >> to
> >> >> >> whom
> >> >> >> >> it
> >> >> >> >> is
> >> >> >> >> addressed. If you believe this e-mail was sent to you in error
> >> and
> >> >> >> the
> >> >> >> >> e-mail
> >> >> >> >> contains patient information, please contact the Partners
> >> >> Compliance
> >> >> >> >> HelpLine at
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> >> >> >> and
> >> >> >> >> properly
> >> >> >> >> dispose of the e-mail.
> >> >> >> >>
> >> >> >> >>
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >> -------------------------
> >> >> >> 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
> >> >>
> >> >
> >>
> >>
> >> -------------------------
> >> 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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