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

dgw dgwakeman at gmail.com
Tue Jun 3 10:54:16 EDT 2014
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Currently the matlab toolbox doesn't have functions to write forward or
inverse solutions. Most development has shifted to mne-python, which does
have functions for both of these.

D


On Tue, Jun 3, 2014 at 10:48 AM, Thinh Nguyen <thinhnguyen0405 at gmail.com>
wrote:

> 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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