[Mne_analysis] mne_make_cor_set - transform problem

Matti Hamalainen msh at nmr.mgh.harvard.edu
Mon Apr 18 11:35:38 EDT 2016
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Hi Don,

You can read the fif file mne_make_cor_set made in mrilab and do the coordinate transformation there as you have used to and produce a new fif file where the transformation is in place.
This does not deal with the different coordinate systems between the one derived from the DICOM files and the mgz files, though.

- Matti

> On Apr 18, 2016, at 11:31 AM, Krieger, Donald N. <kriegerd at upmc.edu> wrote:
> 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 à tkrRAS  rather than Head à 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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Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org

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