[Mne_analysis] Transform stc from head to MRI coordinate system?

[Jon Houck]

        External Email - Use Caution        

Hi Lori,

Are you definitely using the volume source space to compute the forward
solution and inverse operator?  There's not a separate '_volume_' function
for the forward solution or inverse inverse operator, so if you're also
setting up the surface models in the same script it would be very easy to
inadvertently use the surface model or even overwrite the volume output
files (speaking from experience...).  Here's what mine currently looks like:

head = setup_volume_source_space(subject, mri=fname_t1, bem=fname_bem,
mindist=mindist,
                         subjects_dir=subjects_dir, add_interpolator=True)
mne.write_source_spaces(fname_volsrc, head, overwrite=True)

forward = mne.make_forward_solution(fname_raw, fname_trans, head, fname_bem,
                    meg=True, eeg=False, mindist=mindist,
                    n_jobs=8)
mne.write_forward_solution(fname_volfwd, forward, overwrite=True)

inverse_operator = make_inverse_operator(raw.info, forward, noise_cov,
loose=1, depth=None, fixed=False)
write_inverse_operator(fname_volinv, inverse_operator, verbose=True)

Jon



On Wed, May 30, 2018 at 3:15 PM, Lori Sanfratello <lsanfratello at mrn.org>
wrote:

>         External Email - Use Caution
>
> Unfortunately, it seems to revert back to head coordinates at the fwd
> step.  Any other possibilities?
> Thanks,
> Lori
>
> On Tue, May 29, 2018 at 1:45 PM, Lori Sanfratello <lsanfratello at mrn.org>
> wrote:
> > Thanks Eric! I will give it a try.
> > Best,
> > Lori
> >
> > On Tue, May 29, 2018 at 10:12 AM, Eric Larson <larson.eric.d at gmail.com>
> wrote:
> >>         External Email - Use Caution
> >>
> >> I think that if you constructed your volume source space with the `mri`
> >> argument and `add_interpolator=True`, then you should be able to do
> >> `stc.save_as_volume(...)` or `as_volume` that will already properly be
> in
> >> the same MRI coordinates as the `mri` you originally supplied. Does that
> >> help?
> >>
> >> Eric
> >>
> >>
> >> On Mon, May 28, 2018 at 5:42 PM, Lori Sanfratello <lsanfratello at mrn.org
> >
> >> wrote:
> >>>
> >>>         External Email - Use Caution
> >>>
> >>> Hi, I would like my volumetric source estimate to be in MRI
> >>> coordinates, is there a way to easily transform my stc, before I save
> >>> it into nifti?
> >>> Thank you for any advice!
> >>> Best,
> >>> Lori
> >>> --
> >>> Dr. L. Sanfratello, PhD
> >>> Assistant Professor of Trans. Neuroscience
> >>> The Mind Research Network,
> >>> 1101 Yale Blvd NE
> >>> Albuquerque, NM 87106
> >>> 505 272-5557
> >>>
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> >
> > --
> > Dr. L. Sanfratello, PhD
> > Assistant Professor of Trans. Neuroscience
> > The Mind Research Network,
> > 1101 Yale Blvd NE
> > Albuquerque, NM 87106
> > 505 272-5557
>
>
>
> --
> Dr. L. Sanfratello, PhD
> Assistant Professor of Trans. Neuroscience
> The Mind Research Network,
> 1101 Yale Blvd NE
> Albuquerque, NM 87106
> 505 272-5557
>
> _______________________________________________
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