3D brain sagittal MRI

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!


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