[Mne_analysis] mne_make_cor_set - transform problem

Krieger, Donald N. kriegerd at upmc.edu
Mon Apr 18 11:31:37 EDT 2016
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This is a follow-on to a previous post to which Jon Houck helpfully suggested using mne_make_cor_set.
I am using this to convert .mgz files to .fif .
I normally start with the original dicom set and convert them to .fif using ELEKTA's dicom_access.
But for these MEG data sets, I only have a defaced (via freesurfer) .mgz files.

In either case I then use the .fif files to do MEG coregistration with ELEKTA's Mrilab tool.
Using Mrilab is part of my standard pipeline and I would like to stick with that if possible.

When I convert a standard dicom scan series to fif using ELEKTA's dicom_access, the .fif is in MR RAS coordinates.
But a .fif file obtained by conversions from .mgz with mne_make_cor_set appears to be in tkr RAS coordinates instead.
So the transform matrix that I get when I do the coregistration is: Head --> tkrRAS  rather than Head --> RAS  .

I tried spoofing mne_make_cor_set with -talairach SomeOtherTransformation  but Mrilab doesn't appear to care.
In addition, it's not clear to me what transform to use even if it does work; maybe tkr2scanner .

Any thoughts would be welcome and thanks.

Best - Don

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