Spatial tranformations of the anatomical data

Discussions
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1

Hello everyone,

I imported a T1-weighted MRI into Brainstorm along with FreeSurfer's segmentation outputs, which are in the same space as the original T1. I would now like to use the file tess_cortex_pialcereb_low.mat outside of Brainstorm (in MATLAB) for further processing — specifically to compare it with a tractogram that was coregistered with the original T1.
However, I noticed that the coordinates in tess_cortex_pialcereb_low.mat do not match those of my tractogram, even though both should be in the same anatomical space.

  • Does Brainstorm apply any transformation to the surfaces upon import or processing?
  • If so, is there a way to retrieve or apply this transformation?
  • How could I transform the tractogram to put it in the Brainstorm space ?

Thank you very much for your help!

2

Hello @CandiceAppr

Yes, surfaces are stored in SCS coordinates, which are based on the anatomical fiducials
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Subject_Coordinate_System_.28SCS_.2F_CTF.29

The transformation between coordinate systems with the function
cs_convert()

https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems

Have you tried importing your fibers file into Brainstorm?