Change lumbar file from full-body (t2.nii.gz) to lumbar region (t2_lumbar.nii.gz) (#19)

Author: joshuacwnewton

single_subject/batch_single_subject.sh

@@ -217,8 +217,6 @@ 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 -o t2_lumbar.nii.gz
 # Use lumbar-specific `sct_deepseg` model to segment the spinal cord
 sct_deepseg -i t2_lumbar.nii.gz -task seg_lumbar_sc_t2w
 
@@ -229,7 +227,7 @@ sct_deepseg -i t2_lumbar.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_lumbar_labels.nii.gz
+sct_label_utils -i t2_lumbar.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_lumbar.nii.gz \

single_subject/data/t2_lumbar/t2.nii.gz

@@ -5,7 +5,7 @@ data_vertebral-labeling,single_subject/data/t2/t2_seg.nii.gz
 data_template-registration,single_subject/data/t2/t2.nii.gz
 data_template-registration,single_subject/data/t2/t2_seg.nii.gz
 data_template-registration,single_subject/data/t2/t2_labels_vert.nii.gz
-data_lumbar-registration,single_subject/data/t2_lumbar/t2.nii.gz
+data_lumbar-registration,single_subject/data/t2_lumbar/t2_lumbar.nii.gz
 data_shape-metric-computation,single_subject/data/t2/t2_seg.nii.gz
 data_shape-metric-computation,single_subject/data/t2/label/template/PAM50_levels.nii.gz
 data_compression,single_subject/data/t2_compression/t2_compressed.nii.gz