[Mne_analysis] How to modify source space file "*-src.fif"

[Thinh Nguyen]

Thank you all for your help

Given your answers, now I'm wondering if it is possible to write a new .fif
file, say the inverse operator, or forward solution, from Matlab. The
reason I'm asking is because I'm aware that we can export inverse/forward
solution to matlab and view them. But if we were to modify them, customize
them to specific case, is it possible to write that modified mat file into
a .fif file and use that back into the MNE processing pipeline. Can Matlab
do it or does it have to be a Python code?

Best,
Thinh Nguyen


On Sat, May 31, 2014 at 2:13 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> hi Thinh,
>
> reducing the source space to the fMRI ROIs is really dangerous as you
> will "force" the MEG data to be explained with these ROIs.
> Using mne_do_inverse_operator is your only option as far as I know.
> Scaling the source covariance is a soft way to restrict the source space.
>
> Alex
>
>
> On Fri, May 30, 2014 at 9:55 PM, Thinh Nguyen <thinhnguyen0405 at gmail.com>
> wrote:
> > Hi D,
> >
> > Thanks for your reply, I'm trying to reduce the number of active source
> > using fMRI information. I have a txt file, or w file of the sources to do
> > calculation on. The idea is just to remove those source points that are
> > outside of my region of interest, then perform forward and inverse
> > calculation as normal, using the modified source space.
> > I know there is an option to constrain source space in
> > mne_do_inverse_operator, but it seems to give unreasonable results (or at
> > least very confusing results). As to my understanding, the constraints
> > applied in mne_do_inverse_operator modify the source covariance matrix,
> > which is not of interest to me.
> > On the other hand, is there a way to modify the forward matrix, or
> inverse
> > matrix at all? I know we can read them into matlab, but I don't know how
> to
> > modify the *.fif file itself.
> >
> > Thanks
> > Thinh
> >
> >
> > On Fri, May 30, 2014 at 2:44 PM, dgw <dgwakeman at gmail.com> wrote:
> >>
> >> Hi Thinh,
> >>
> >> Typically, constraints are applied either to the forward matrix or
> inverse
> >> matrix. Can you let us know what type of constraint you are trying to
> add,
> >> so we might be able to help you better?
> >>
> >> Thanks,
> >> D
> >>
> >>
> >>
> >> On Fri, May 30, 2014 at 3:42 PM, Thinh Nguyen <
> thinhnguyen0405 at gmail.com>
> >> wrote:
> >>>
> >>> Hi MNE users,
> >>>
> >>> Does anyone know how to modify the source space created in
> >>> mne_setup_source_space step.
> >>> MNE does create txt file version of the source space for visualization
> >>> purposes, but I can't seem to find anyway to modify the src.fif file
> itself.
> >>> I want to try applying a prior constraints onto the source space.
> Thank you
> >>>
> >>> Sincerely,
> >>> Thinh Nguyen
> >>>
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