Problem about measure the CSA of upper spinal cord in the MP2RAGR

SCT
1

Hi Julien
I was trying to caculate the CSA of upper spine cord in the T1 map,the sequence is MP2RAGE.I found it isn’t recongnize the spine cord.Is there any ways to solve this problem?Here is my code.
echo 1 spinal cord segmentation
sct_deepseg_sc -i T1.nii.gz -c t1
echo 2 label vertebrae
sct_label_vertebrae -i T1.nii.gz -s T1_seg.nii.gz -c t1
echo 3 Compute CSA at C2-C3 levels
sct_process_segmentation -i T1_seg.nii.gz -p csa -vert 2:3 -vertfile T1_seg_labeled.nii.gz

Best,
Jenny

2

Hi Jenny,
could you try with one of the T1w of the MP2RAGE? The deep learning model is trained on the T1w, so it should work better.
Cheers,
Julien