batch_single_subject.sh: Fix lumbar filenames

single_subject/batch_single_subject.sh

@@ -218,9 +218,9 @@ sct_register_multimodal -i t1_crop.nii.gz -d ../t2/t2_crop.nii.gz -param step=1,
 cd ../t2_lumbar
 
 # Crop full-body image to isolate the lumbar region (lowest 200 axial slices)
-sct_crop_image -i t2.nii.gz -zmax 200
+sct_crop_image -i t2.nii.gz -zmax 200 -o t2_lumbar.nii.gz
 # Use lumbar-specific `sct_deepseg` model to segment the spinal cord
-sct_deepseg -i t2_crop.nii.gz -task seg_lumbar_sc_t2w
+sct_deepseg -i t2_lumbar.nii.gz -task seg_lumbar_sc_t2w
 
 # Generate labels for the 2 spinal cord landmarks: cauda equinea ('99') and T9-T10 disc ('17')
 # Note: Normally this would be done manually using fsleyes' "Edit mode -> Create mask" functionality. (Uncomment below)
@@ -229,12 +229,12 @@ 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.nii.gz -create 22,77,187,17:27,79,80,60 -o t2_crop_labels.nii.gz
+sct_label_utils -i t2.nii.gz -create 22,77,187,17:27,79,80,60 -o t2_lumbar_labels.nii.gz
 
 # Register the image to the template using segmentation and labels
-sct_register_to_template -i t2_crop.nii.gz \
-                         -s t2_crop_seg.nii.gz \
-                         -ldisc t2_crop_label.nii.gz \
+sct_register_to_template -i t2_lumbar.nii.gz \
+                         -s t2_lumbar_seg.nii.gz \
+                         -ldisc t2_lumbar_labels.nii.gz \
                          -c t2 -qc qc \
                          -param step=1,type=seg,algo=centermassrot:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=3,slicewise=0:step=3,type=im,algo=syn,metric=CC,iter=3,slicewise=0