7T spinal cord segmentation

Hi all,

I am working with 7T spinal cord data that is more challenging to process because of significant B1+ variations along the cord (it was acquired using an array of surface coils). Julien kindly worked with the data and came up with the following approach. I am posting the code (and resultant 7T segmentation) here so that it may be available as a resource for the SCT community.



sct_resample -i t2.nii -mm 0.5
sct_propseg -i t2_r.nii -c t2 -min-contrast 10
sct_smooth_spinalcord -i t2_r.nii -s t2_r_seg.nii -smooth 0,0,5
sct_maths -i t2_r_smooth.nii -mul t2_r_smooth.nii -o t2_r_smoothmul.nii
sct_deepseg_sc -i t2_r_smoothmul.nii -c t2 -centerline file -file_centerline t2_r_seg.nii -kernel 2d -qc qc

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