This results in a suboptimal cropping (removing top and bottom slices):
Crop using the SC seg
On the other, when trying the centerline (sct_get_centerline), I get the following:
# Get the centerline
sct_get_centerline -i "${file_dwi}"_dwi_mean.nii.gz -c dwi
# Crop data around the centerline for faster processing
sct_crop_image -i "${file_dwi}".nii.gz -m "${file_dwi}"_dwi_mean_centerline.nii.gz -dilate 25x25x0 -o "${file_dwi}"_crop.nii.gz
SC seg on the mean DWI image (
"${file_dwi}"_dwi_mean) using the contrast-agnostic model misses the top and bottom slices with severe signal dropouts.https://github.com/valosekj/dcm-brno/blob/3cf9697a1c413a2a834543e36bf6857d15494196/scripts/01_process_data.sh#L330-L334
DWI mean SC seg
This results in a suboptimal cropping (removing top and bottom slices):
Crop using the SC seg
On the other, when trying the centerline (
sct_get_centerline), I get the following:Crop using the centerline