batch_single_subject.sh: Restore sct_warp_template commands

This is done to match the slides, even though the ordering is slightly
different in the webpage tutorials.

Author: joshuacwnewton

single_subject/batch_single_subject.sh

@@ -208,21 +208,20 @@ sct_extract_metric -i t2s.nii.gz -f t2s_gmseg.nii.gz -method bin -z 2:12 -o t2s_
 # Register template->t2s (using warping field generated from template<->t2 registration)
 # Tips: Here we use the WM seg for the iseg/dseg fields in order to account for both the cord and the GM shape.
 sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_wm.nii.gz" -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
+# Warp template
+sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz -qc ~/qc_singleSubj
 
 cd ../mt
 # Register template->mt via t2s to account for GM segmentation
 sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
-
-
+# Warp template
+sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -qc ~/qc_singleSubj
+# Check results
+fsleyes mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 100.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 100.0 &
 
 # Atlas-based analysis (Extracting metrics (MTR) in gray/white matter tracts)
 # ======================================================================================================================
 
-# In order to use the PAM50 atlas to extract/aggregate image data, the atlas must first be transformed to the MT space
-sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc ~/qc_singleSubj
-# Check results
-fsleyes mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 100.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 100.0 &
-
 # Extract MTR for each slice within the white matter (combined label: #51)
 # Tips: To list all available labels, type: "sct_extract_metric"
 sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 51 -o mtr_in_wm.csv