[Mne_analysis] Mne_analysis Digest, Vol 120, Issue 39

[Luke Bloy]

Hi Allison,

I have only used the python tools as well, but using these tools I have
been able to make sense of the various transforms.

My work flow is roughly
1) put the digitization file inside the ds folder.
2) use mne.io.read_raw_ctf to load the data
3) use mne.io.write_info to write out an info.fif file.
4) do mne coreg using the info fif file with the points.
5) the digitization points in the MNE_HEAD_COORD frame are stored in the
info['dig'] structure. you can apply the trans file you saved as part of
mne coreg to get to freesurfer TKR MRI space, and then use transforms in
the T1.mgz file (via nibabel) to get to standard MRI space.

Here is a gist (
https://gist.github.com/bloyl/13cc7e78625ab8b262ab43dab8a05175) that prints
out the dig points in TKR space. and could serve as a basis to do what you
need.

If there is interest I can also share some routines I use to write out
points to a slicer3d fscv file in standard MRI world RAS space.

-Luke


On Wed, Jan 31, 2018 at 3:10 AM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

> hi Allison,
>
> I have never used CTF data with mne unix command line tools. Just in Python
> using the SPM dataset.
>
> you can read the CTF data from python and if all goes well you should have
> the infos you need in the info['dig']. Otherwise you can update the
> content of this.
>
> sorry not to be able to help more.
>
> maybe someone here has more experience with CTF data using MNE.
>
> ALex
>
> On Tue, Jan 30, 2018 at 9:06 PM, Nugent, Allison C. (NIH/NIMH) [E]
> <nugenta at mail.nih.gov> wrote:
> > 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
> >
> >
> >
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