[Mne_analysis] mne_make_cor_set - transform problem

Matti Hamalainen msh at nmr.mgh.harvard.edu
Mon Apr 18 12:00:26 EDT 2016
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Hi Don,

In fact, the coordinate transformation between the scanner coordinates and surface RAS coordinates is in the file produced my mne_make_cor_set. 
You can see this when you do 

mne_show_fiff —verbose —tag 222 —in <filename>

To my understanding, it is only a displacement.

- Matti

> On Apr 18, 2016, at 11:53 AM, Krieger, Donald N. <kriegerd at upmc.edu> wrote:
> 
> Hi Matti,
>  
> Thanks for responding so quickly.
> I tried what you suggest for a scan for which I have dicoms.
> I created 2 .fif’s, one with dicom_access and one with mne_make_cor_set.
>  
> Here are the two transforms grabbed with show_fiff:
> # dicom_access
> # 222 = transform         head -> MRI
> #         0.999356 0.028735 -0.021495
> #         -0.035189 0.902169 -0.429945
> #         0.007038 0.430425 0.902599
> #         -4.798210 8.148447 -50.913933 (inv. 5.440169 14.701207 49.355110)
> # mne_make_cor_set
> # 222 = transform         head -> MRI
> #         0.999505 0.024229 0.020096
> #         -0.014078 0.915056 -0.403080
> #         -0.028155 0.402598 0.914944
> #         -3.010607 -9.352709 -35.697933 (inv. 1.872374 23.003098 28.952219)
>  
> I guess the rotations look pretty much the same and if I apply the tkr2scanner transform to the displacement, -3.010607 -9.352709 -35.697933, I get
> -5.14 6.311 -52.083 which is also pretty good.
>  
> That’s encouraging actually.  Do you see any way to get it to kick out the correct displacements?
>  
> Don
>  
>  
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Matti Hamalainen
> Sent: Monday, April 18, 2016 11:36 AM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] mne_make_cor_set - transform problem
>  
>  
> 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 <mailto: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 <mailto:msh at nmr.mgh.harvard.edu>
> mhamalainen at partners.org <mailto:mhamalainen at partners.org>
> 
> 
> 
> 
> 
>  
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