Draw T1W slice with left/right, anterior/posterior, superior/inferior tags

1

Hello!
I have a structural dataset with messed up orientation. When I open them in Mango or FSLView I can see that Left/Right, Anterior/Posterior, Superior/Inferior do not always correspond with the real orientation of the data. I could just open each MRI volume 1 by 1 but it would take forever…

Is there a way of python scripting something that would save sagittal, coronal and axial slices with L/R, A/P, S/I annotated? I tried using nibabel, but the tutorial code I had found only prints data in voxel space, and if I had applied the affine matrix before, the data space could potentially be oblique…

Thanks in advance for your help!

2

For the moment I’m using slicer from FSL, but (1) I’d prefer to stay in python and (2) slicer sometimes gets the orientation wrong…

3

Found the solution, using the awesome nilearn

from nilearn import plotting
plotting.plot_anat("anat.nii.gz",output_file="anat.png");

This guy should be turned into a command line. It’s much better than slicer (for what i was aiming to do)