Straightening Spine on 3D T1 brain images

Hello everyone! I am new to SCT and I was wondering is there a way to use it in order to straighten spine on brain 3d t1 images?

Hi @Stefan_Radonjic,

Absolutely, the procedure is the same as in the example batch_processing: first, segment the cord, and then run sct_straighten_spinalcord. Note that this procedure will get rid of the brain part, because there is no “centerline” for the brain. Example below:

sct_download_data -d sct_example_data
cd sct_example_data/t1
sct_deepseg_sc -i t1.nii.gz -c t1
sct_straighten_spinalcord -i t1.nii.gz -s t1_seg.nii.gz