batch_single_subject.sh: Use command from tutorial

joshuacwnewton · web-flow · commit 8c7b4c1520ca · 2023-10-16T14:39:37.000-04:00
See: spinalcordtoolbox/spinalcordtoolbox@cd7f284
diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh
@@ -164,8 +164,7 @@ sct_deepseg -i t2_crop.nii.gz -task seg_lumbar_sc_t2w
 #
 # However, since this is an automated script with example data, we will place the labels at known locations for the
 # sake of reproducing the results in the tutorial.
-sct_label_utils -i t2_crop.nii.gz -create 27,80,80,60 -o t2_crop_label.nii.gz
-sct_label_utils -i t2_crop_label.nii.gz -create-add 27,76,187,17 -o t2_crop_label.nii.gz
+sct_label_utils -i t2.nii.gz -create 22,77,187,17:27,79,80,60 -o t2_crop_labels.nii.gz
 
 # Register the image to the template using segmentation and labels
 # TODO: Uncomment when https://github.com/spinalcordtoolbox/PAM50/pull/27 gets merged and a new PAM50 release is made.

Original file line number	Diff line number	Diff line change
`@@ -164,8 +164,7 @@ sct_deepseg -i t2_crop.nii.gz -task seg_lumbar_sc_t2w`
`164`	`164`	`#`
`165`	`165`	`# However, since this is an automated script with example data, we will place the labels at known locations for the`
`166`	`166`	`# sake of reproducing the results in the tutorial.`
`167`		`-sct_label_utils -i t2_crop.nii.gz -create 27,80,80,60 -o t2_crop_label.nii.gz`
`168`		`-sct_label_utils -i t2_crop_label.nii.gz -create-add 27,76,187,17 -o t2_crop_label.nii.gz`
	`167`	`+sct_label_utils -i t2.nii.gz -create 22,77,187,17:27,79,80,60 -o t2_crop_labels.nii.gz`
`169`	`168`
`170`	`169`	`# Register the image to the template using segmentation and labels`
`171`	`170`	`# TODO: Uncomment when https://github.com/spinalcordtoolbox/PAM50/pull/27 gets merged and a new PAM50 release is made.`