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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
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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
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Thanks Eric! I will give it a try.
Best,
Lori
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Unfortunately, it seems to revert back to head coordinates at the fwd
step. Any other possibilities?
Thanks,
Lori
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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