Hello SCT Forum,
We have some sagittal dedicated brain acquisitions that capture up to C5 and we woud like to run SCT. Does the commands series to launch sct_deepseg_sc differ from a more traditional dedicated sagittal spinal cord acquisition ? I.e. are there specific flags labeling in the input as such ?
Thank you!
Mathilde
Hi Mathilde,
“Sagittal” only refers to the orientation of the FOV. What matters in the end is the right-left resolution. For example, a 3D MPRAGE acquired sagittally at 1mm isotropic is equivalent to an axial orientation (in terms of partial volume across all three dimensions).
However, a sagittal scan acquired with a 2D sequence, at 0.5x0.5x3 mm resolution does not provide the same definition of the spinal cord in the right-left dimension, and hence is much more difficult to reliably segment.
If you find yourself in the former case, then sure, you can give sct_deepseg_sc a try. If you find the results unsatisfactory, we have a new model that you can already try using:
sct_deepseg -i IMAGE -task seg_sc_contrast_agnostic
Cheers,
Julien