`philadelphia-pediatric` - swapped R-L axis for `rec-composed` images?
valosekj opened this issue · 0 comments
valosekj commented
When fixing qform and sfrom matrices for the newly shared data (details: #334 (comment)), I noticed that the existing rec-composed_T2w
images might also have a swapped R-L axis compared to the acq-top_run-1_T2w
and acq-bottom_run-1_T2w
images.
Let's check, for example, sub-123
by the following commands:
cd philadelphia-pediatric/sub-123/anat
# reorient the composed image (which is AIL) to LPI to match the orientation of acq-top and acq-bottom images to allow easy visual comparison
sct_image -i sub-123_rec-composed_T2w.nii.gz -setorient LPI -o sub-123_rec-composed_T2w_LPI.nii.gz
# Open three separate FSLeyes
ff sub-123_rec-composed_T2w_LPI.nii.gz & ff sub-123_acq-top_run-1_T2w.nii.gz & ff sub-123_acq-bottom_run-1_T2w.nii.gz
Now, you locate the subtle scoliosis in all images and compare the R-L axis. If I am not mistaken, I believe that the R-L labels in the composed image should actually be L-R.
GIF comparing rec-composed and acq-top
Notice the different directions of the spinal cord centerline between images while the R-L labels are still the same.
Do we have more details on how the rec-composed_T2w
images were created?
Relevant comment to see: #334 (comment)