Update batch_single_subject.sh and process_data.sh to match changes to 2024 SCT Course Slides (#25)

Co-authored-by: Jan Valosek <39456460+valosekj@users.noreply.github.com>
Co-authored-by: Kalum Ost <43527660+SomeoneInParticular@users.noreply.github.com>

Author: 3 people

.github/workflows/run_batch_script.yml

@@ -62,10 +62,26 @@ jobs:
             fi
         done
 
-    - name: Check that script executed without error
+    - name: Check results (no error logs)
+      if: always()
       run: |
         cd "${{ github.event.repository.name }}/multi_subject/output/log"
         [ "$(compgen -G "process_data_sub-0*.log")" ]        # Log files should exist
+
+    - name: Check results (no error logs)
+      if: always()
+      run: |
+        cd "${{ github.event.repository.name }}/multi_subject/output/log"
         [ ! "$(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
+
+    - name: Check results (warnings in log)
+      if: always()
+      run: |
+        cd "${{ github.event.repository.name }}/multi_subject/output/log"
+        # ! grep -iF "warning" process_data_sub-01.log
+
+    - name: Check results (errors in log)
+      if: always()
+      run: |
+        cd "${{ github.event.repository.name }}/multi_subject/output/log"
+        ! grep -iF "error" process_data_sub-01.log

multi_subject/process_data.sh

@@ -71,7 +71,6 @@ segment_if_does_not_exist() {
   #  This allows you to add manual segmentations on a subject-by-subject basis without disrupting the pipeline.
   ###
   local file="${1}"
-  local contrast="${2}"
   # Update global variable with segmentation file name
   FILESEG="${file}"_seg
   FILESEGMANUAL="${PATH_DATA}"/derivatives/labels/"${SUBJECT}"/anat/"${FILESEG}".nii.gz
@@ -84,7 +83,7 @@ segment_if_does_not_exist() {
   else
     echo "Not found. Proceeding with automatic segmentation."
     # Segment spinal cord
-    sct_deepseg_sc -i "${file}".nii.gz -c "${contrast}" -qc "${PATH_QC}" -qc-subject "${SUBJECT}"
+    sct_deepseg -task seg_sc_contrast_agnostic -i "${file}".nii.gz -qc "${PATH_QC}" -qc-subject "${SUBJECT}"
   fi
 }
 
@@ -111,8 +110,8 @@ rsync -avzh "${PATH_DATA}"/"${SUBJECT}" .
 # ======================================================================================================================
 cd "${SUBJECT}"/anat/
 file_t2="${SUBJECT}"_T2w
-# Segment spinal cord (only if it does not exist)
-segment_if_does_not_exist "${file_t2}" "t2"
+# Segment spinal cord (only if it does not exist) using contrast-agnostic model
+segment_if_does_not_exist "${file_t2}"
 file_t2_seg="${FILESEG}"
 # Create labels in the cord at C2 and C5 mid-vertebral levels (only if it does not exist)
 label_if_does_not_exist "${file_t2}" "${file_t2_seg}"
@@ -132,8 +131,8 @@ sct_process_segmentation -i "${file_t2_seg}".nii.gz -vert 2:3 -vertfile label_T2
 # ======================================================================================================================
 file_mt1="${SUBJECT}"_acq-MTon_MTS
 file_mt0="${SUBJECT}"_acq-MToff_MTS
-# Segment spinal cord
-segment_if_does_not_exist "${file_mt1}" "t2s"
+# Segment spinal cord using contrast-agnostic model
+segment_if_does_not_exist "${file_mt1}"
 file_mt1_seg="${FILESEG}"
 # Create mask
 sct_create_mask -i "${file_mt1}".nii.gz -p centerline,"${file_mt1_seg}".nii.gz -size 45mm