Create cord segmentations

[jcohenadad]

for center/study:

• paris_2017-*

Todo:

• drag/drop folder on local station
• open terminal
• cd to folder of image
• segment using propseg. Ex for t2-w contrast:

sct_propseg -i t2.nii.gz -c t2 -init-centerline viewer
sct_propseg -i t2.nii.gz -c t2 -init-centerline viewer -radius 6  # if segmentation too small in axial plane
sct_propseg -i t2.nii.gz -c t2 -init-centerline viewer -min-contrast 20  # if segmentation not long enough caudally

• Check output segmentation, and correct if necessary. Use sag+axial views. Use CMD+F to switch on/off the seg. Use ALT+E to activate edit mode.
• Save as *_seg_manual.nii.gz
• Remove unecessary files (only keep image + image_seg_manual)
• Add seg in the DB
• Julien will copy the seg on sct_testing