Merge branch 'master' into jn/12-improve-double-quoting

.github/workflows/run_batch_script.yml

@@ -53,12 +53,19 @@ jobs:
     - name: Output full log for sanity checking
       run: |
         cd "${{ github.event.repository.name }}/multi_subject/output/log"
-        cat process_data_sub-01.log
+        for logfile in process_data_sub-01.log err.process_data_sub-01.log; do
+            if [[ -e "${logfile}" ]]; then
+                echo "=== Contents of ${logfile} ==="
+                cat "${logfile}"
+            else
+                echo "=== No file ${logfile} ==="
+            fi
+        done
 
     - name: Check that script executed without error
       run: |
         cd "${{ github.event.repository.name }}/multi_subject/output/log"
         [ "$(compgen -G "process_data_sub-0*.log")" ]        # Log files should exist
         [ ! "$(compgen -G "err.process_data_sub-0*.log")" ]  # Error files should NOT exist
         grep -iF "warning" process_data_sub-01.log
-        grep -iF "error" process_data_sub-01.log
+        grep -iF "error" process_data_sub-01.log

multi_subject/process_data.sh

@@ -145,9 +145,12 @@ file_mt1="${file_mt1}"_crop
 # Tips: here we only use rigid transformation because both images have very
 # similar sequence parameters. We don't want to use SyN/BSplineSyN to avoid
 # introducing spurious deformations.
-sct_register_multimodal -i "${file_mt0}".nii.gz -d "${file_mt1}".nii.gz \
+sct_register_multimodal -i "${file_mt0}".nii.gz \
+                        -d "${file_mt1}".nii.gz \
+                        -dseg "${file_mt1}"_seg.nii.gz \
                         -param step=1,type=im,algo=rigid,slicewise=1,metric=CC \
-                        -x spline -qc "${PATH_QC}"
+                        -x spline \
+                        -qc "${PATH_QC}"
 # Register template->mt1
 # Tips: here we only use the segmentations due to poor SC/CSF contrast at the bottom slice.
 # Tips: First step: slicereg based on images, with large smoothing to capture