Neuromag coordinate frames

Gustavo Sudre gsudre at POBOX.COM
Tue Sep 1 21:16:13 CEST 2009


I have a question about the transformation matrix used when reading in
Neuromag FIF MRI files. Looking at the read_mri function, the matrix
stored in hdr.trans.trans by MNE toolbox is copied to mri.transform.
The fieldtrip wiki says that the matrix in mri.transform transforms
from the native voxel-coordinate system of the MRI to the head
coordinate system. However, the matrix stored in hdr.trans.trans goes
from 4 to 5 (as seen in mri.hdr.trans), which means from head to MRI.
So, shouldn't mri.transform = inv(hdr.trans.trans)?

Please let me know if I'm mistaken on how the coordinate systems
interact in these toolboxes.

Thank you,


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