MRi image orientation

Discussions
1

Hi Francois and other Brainstorm users,

I am loading an MRI file that has a tilt in the image orientation:
nfo.ImagePositionPatient : 84.5000 -153.4595 107.6982
nfo.ImageOrientationPatient: 0 0.9963 0.0857 0 0.0857 -0.9963

The above numbers are coming from the dicom header. When loading the mri in Brainstorm, it detects it and asks “A transformation is available in the MRI file. Do you want to apply it to the volume now?”.

Can you tell me:

  1. what is the exact transformation that is performed? is it only direction flipping or the rotation is also performed? where is the transformation matrix saved?
  2. is the same transformation performed in all subsequent surfaces and masks that are added to the patient’s anatomy?

Thanks,
Cristi

2

Hi Cristi,

The transformation that you have is not exactly the one from the DICOM, but the one from the .nii file that you created from them.
When importing the .nii volume in Brainstorm, the transformation available in the file is simplified to keep only 90 degree rotations (= dimension transpositions) and flips along the three dimensions.
The goal is to bring the volume closer to the orientation brainstorm expects (http://neuroimage.usc.edu/brainstorm/CoordinateSystems#MRI_coordinates)

This transformation is not stored anywhere. If you need more details, you can follow directly from the code what is happening.
It is handled in function brainstorm3/toolbox/io/in_mri_nii.m, lines 134-164. Place a breakpoint at the beginning, import your file, then follow the execution step by step.

This transformation is not applied to any other volume or surface after.
The correct procedure for importing the anatomy and make sure that everything is imported correctly is to use the menu “Import anatomy folder” and select the segmentation folder generated by FreeSurfer, BrainSuite or BrainVISA.
You can check that the surfaces are correctly aligned with the volume after. Right-click on the cortex surface > MRI registration > Check MRI/surface registration.

Cheers,
Francois

3

Hi,
Im sorry for the late replay. It helped i manually applied the same transformation to the other surfaces , thank you.
Best,
Cristi