[Mne_analysis] Mne_analysis Digest, Vol 120, Issue 39

[Nugent, Allison C. (NIH/NIMH) [E]]

Hi Alex - thanks for your response!
I've resolved part of my problem, and I think I have figured out what I really need.
What I really need is to get the location of the fiducials from the digitizer space into mri space.  

I have used mne_ctf_dig2fiff to put a text version of a Polhemus digitizer file into .fif format.  I do not know the coordinate frame that these points are transformed to, if any.  
I have a freesurfer surface, with mri fiducials saved in a .fif file (this appears to be in the TkReg RAS coordinate frame, in meters)
I used mne coreg to line up the digitizer head shape (including the marked fiducials) with the MRI.

Now, I want the coordinates of the fiducials marked using the digitizer in MRI space.  
These are obviously created by mne coreg, because they are plotted on the surface, I believed they are saved internally as transformed_hsp_nasion, etc.  If there is any way to easily get these coordinates that would be fantastic. 

I have tried:
If, for instance, the location of the nasion coil that I put in .fif format with mne_ctf_dig2fiff is stored in a variable nasion_xyz,  
mne.transforms.apply_trans(trans_head_mri,nasion_xyz)
where trans_head_mri is the transform saved when I press the "Save As..." button in mne coreg

But this does not produce coordinates that are in the same coordinate frame as the MRI. This makes me think that mne_ctf_dig2fiff is transferring the coordinates to a different coordinate frame, but I don't know which one. 

Anyway, the upshot of all this is that I need a way to get the coordinates of the headshape file fiducials in MRI space.  If there's an easier way to do this, or a more transparent way of getting the headshape file into mne, let me know. 
Thanks!

Allison

-----Original Message-----
Date: Sun, 28 Jan 2018 21:33:47 +0100
From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Subject: Re: [Mne_analysis] mne_analyze and mne coreg and
	transformation	matricees
hi Allison,

with "mne coreg" you should not need to convert your data and should be able to work just with .ds raw files.
we currently ship the SPM face dataset which is a CTF dataset.
See:
https://martinos.org/mne/stable/auto_examples/datasets/plot_spm_faces_dataset.html
maybe this can give you a hint of how your data should look like.
don't hesitate to share coreg screenshots.

Alex