[Mne_analysis] MNE in Matlab

Sheraz Khan, PhD sheraz at nmr.mgh.harvard.edu
Wed Jan 31 09:12:23 EST 2018
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The key in assembling inverse is to control regularization, which is
normally the factor of number of trials, since raw data is just single
trial more regularization is needed compare to evoked.
Regularization provide stability to the inverse operator at the expense of
sptial resolution.

Hope this help

Sheraz


> Hi again,
>
> Just my last question regarding this issue: you mentioned that "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.". Could you expand a bit on this? How can I control how to
> assemble the inv operator as "general"?
>
> Thanks,
> Ade
>
> On 26 January 2018 at 23:27, Adela Glez. <adelaglezcom at gmail.com> wrote:
>
>> 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.e
>>> du/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_analys
>>> is
>>> >> >> >> >>
>>> >> >> >> >>
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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
>>> >> >>
>>> >> >
>>> >>
>>> >>
>>> >> -------------------------
>>> >> 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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