# MNE source points in the MRI coordinate system **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [October 21, 2014, 11:14am UTC](https://mne.discourse.group/t/mne-source-points-in-the-mri-coordinate-system/855 "2014-10-21T11:14:10Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 21, 2014, 11:14am UTC](https://mne.discourse.group/t/mne-source-points-in-the-mri-coordinate-system/855/1 "2014-10-21T11:14:10Z")
Dear MNE users, I am trying to transform the coordinates of the MNE source points (in "Head coordinates") of a subject to the coordinate system of the original anatomical MR image of the subject (in "RAS coordinates"?). Following the description in the manual ([http://martinos.org/mne/stable/manual/forward.html](http://martinos.org/mne/stable/manual/forward.html)) it seems that I have to apply two coordinate transformations to these points: from "Head coordinates" to "Surface RAS coordinates" and from "Surface RAS" to "RAS coordinates". I have extracted the two transformations by using these commands: mne\_show\_fiff --in example\_subject/mri/T1-neuromag/sets/COR.fif --verbose mne\_make\_cor\_set --mgh example\_subject/mri/orig.mgz --verbose The commands output the following lines: head -\> MRI (surface RAS)   0.99551 -0.04669 -0.08235 0.57   0.02221 0.96082 -0.27627 -13.19   0.09202 0.27320 0.95754 -22.42   0.00000 0.00000 0.00000 1.00 Coordinate transformation: MRI (surface RAS) -\> RAS (non-zero origin)    1.000000 0.000000 0.000000 0.46 mm    0.000000 1.000000 0.000000 42.65 mm    0.000000 0.000000 1.000000 -11.77 mm    0.000000 0.000000 0.000000 1.00 If I understood correctly, applying these transformations to the coordinates of the MNE source points listed in the file 'example\_subject-7-lh.pnt' in the bem directory should then give me the source points in the original MRI coordinate system. However, these transformed coordinates are nowhere near the cortical surface in the original anatomical MR image (they are off tens of centimeters). (the first few lines of the 'example\_subject-7-lh.pnt' file are as follows: # CoordinateSystem "Head" # X (mm) Y (mm) Z (mm) -15.949615 -101.250862 10.354758 -11.817389 -99.757225 24.933018 -8.782373 -99.445816 11.100106 -15.355161 -100.348282 7.023144 ...) Where is the error in these steps? Is there an easier way to get the MNE source points in the original anatomical MRI coordinate system? Any help clarifying these coordinate systems and their transformations is appreciated. Thanks, --Jukka Saari ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 21, 2014, 12:10pm UTC](https://mne.discourse.group/t/mne-source-points-in-the-mri-coordinate-system/855/2 "2014-10-21T12:10:16Z")
The easiest way is to read the source spaces from the source space file in Matlab or Python. The coordinates are then directly the surface RAS coordinates and a simple origin shift is needed to transform to the non-zero origin RAS. - Matti ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 21, 2014, 2:47pm UTC](https://mne.discourse.group/t/mne-source-points-in-the-mri-coordinate-system/855/3 "2014-10-21T14:47:52Z")
Reading the source points from the file example\_subject-7-src.fif in Python and transforming these points with the Surface RAS -\> RAS transformation solved the problem. Thank you! --Jukka