From be91535a052e9c183f0b31e60cd775f55bc52814 Mon Sep 17 00:00:00 2001
From: Sandrine Bedard <sandrine.bedard@polymtl.ca>
Date: Fri, 26 Jan 2024 13:44:59 -0500
Subject: [PATCH 1/5] rename CSF segmentations

---
 ..._csfseg-manual.json => sub-barcelona05_T2w_label-CSF_seg.json} | 0
 ...seg-manual.nii.gz => sub-barcelona05_T2w_label-CSF_seg.nii.gz} | 0
 ..._T2w_csfseg-manual.json => sub-cmrrb03_T2w_label-CSF_seg.json} | 0
 ..._csfseg-manual.nii.gz => sub-cmrrb03_T2w_label-CSF_seg.nii.gz} | 0
 ...T2w_csfseg-manual.json => sub-geneva04_T2w_label-CSF_seg.json} | 0
 ...csfseg-manual.nii.gz => sub-geneva04_T2w_label-CSF_seg.nii.gz} | 0
 ...2w_csfseg-manual.json => sub-nottwil01_T2w_label-CSF_seg.json} | 0
 ...sfseg-manual.nii.gz => sub-nottwil01_T2w_label-CSF_seg.nii.gz} | 0
 ...2w_csfseg-manual.json => sub-nottwil03_T2w_label-CSF_seg.json} | 0
 ...sfseg-manual.nii.gz => sub-nottwil03_T2w_label-CSF_seg.nii.gz} | 0
 ...2w_csfseg-manual.json => sub-nottwil04_T2w_label-CSF_seg.json} | 0
 ...sfseg-manual.nii.gz => sub-nottwil04_T2w_label-CSF_seg.nii.gz} | 0
 ..._T2w_csfseg-manual.json => sub-pavia04_T2w_label-CSF_seg.json} | 0
 ..._csfseg-manual.nii.gz => sub-pavia04_T2w_label-CSF_seg.nii.gz} | 0
 ...2w_csfseg-manual.json => sub-perform02_T2w_label-CSF_seg.json} | 0
 ...sfseg-manual.nii.gz => sub-perform02_T2w_label-CSF_seg.nii.gz} | 0
 ...fseg-manual.json => sub-tokyoIngenia05_T2w_label-CSF_seg.json} | 0
 ...-manual.nii.gz => sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz} | 0
 ...fseg-manual.json => sub-tokyoIngenia06_T2w_label-CSF_seg.json} | 0
 ...-manual.nii.gz => sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz} | 0
 20 files changed, 0 insertions(+), 0 deletions(-)
 rename derivatives/labels/sub-barcelona05/anat/{sub-barcelona05_T2w_csfseg-manual.json => sub-barcelona05_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-barcelona05/anat/{sub-barcelona05_T2w_csfseg-manual.nii.gz => sub-barcelona05_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-cmrrb03/anat/{sub-cmrrb03_T2w_csfseg-manual.json => sub-cmrrb03_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-cmrrb03/anat/{sub-cmrrb03_T2w_csfseg-manual.nii.gz => sub-cmrrb03_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-geneva04/anat/{sub-geneva04_T2w_csfseg-manual.json => sub-geneva04_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-geneva04/anat/{sub-geneva04_T2w_csfseg-manual.nii.gz => sub-geneva04_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-nottwil01/anat/{sub-nottwil01_T2w_csfseg-manual.json => sub-nottwil01_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-nottwil01/anat/{sub-nottwil01_T2w_csfseg-manual.nii.gz => sub-nottwil01_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-nottwil03/anat/{sub-nottwil03_T2w_csfseg-manual.json => sub-nottwil03_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-nottwil03/anat/{sub-nottwil03_T2w_csfseg-manual.nii.gz => sub-nottwil03_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-nottwil04/anat/{sub-nottwil04_T2w_csfseg-manual.json => sub-nottwil04_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-nottwil04/anat/{sub-nottwil04_T2w_csfseg-manual.nii.gz => sub-nottwil04_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-pavia04/anat/{sub-pavia04_T2w_csfseg-manual.json => sub-pavia04_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-pavia04/anat/{sub-pavia04_T2w_csfseg-manual.nii.gz => sub-pavia04_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-perform02/anat/{sub-perform02_T2w_csfseg-manual.json => sub-perform02_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-perform02/anat/{sub-perform02_T2w_csfseg-manual.nii.gz => sub-perform02_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-tokyoIngenia05/anat/{sub-tokyoIngenia05_T2w_csfseg-manual.json => sub-tokyoIngenia05_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-tokyoIngenia05/anat/{sub-tokyoIngenia05_T2w_csfseg-manual.nii.gz => sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz} (100%)
 rename derivatives/labels/sub-tokyoIngenia06/anat/{sub-tokyoIngenia06_T2w_csfseg-manual.json => sub-tokyoIngenia06_T2w_label-CSF_seg.json} (100%)
 rename derivatives/labels/sub-tokyoIngenia06/anat/{sub-tokyoIngenia06_T2w_csfseg-manual.nii.gz => sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz} (100%)

diff --git a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.json b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.json
rename to derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.json b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.json
rename to derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.json b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.json
rename to derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.json b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.json
rename to derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.json b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.json
rename to derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.json b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.json
rename to derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.json b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.json
rename to derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.json b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.json
rename to derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.json b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.json
rename to derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
diff --git a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_csfseg-manual.json b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.json
similarity index 100%
rename from derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_csfseg-manual.json
rename to derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.json
diff --git a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
similarity index 100%
rename from derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_csfseg-manual.nii.gz
rename to derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz

From 79e7157a149fe8a73af5d9f18ec3ccfad9ccc901 Mon Sep 17 00:00:00 2001
From: Sandrine Bedard <sandrine.bedard@polymtl.ca>
Date: Mon, 5 Feb 2024 10:05:23 -0500
Subject: [PATCH 2/5] add code to fix csf orientation and pixdim to correspond
 with image native space

---
 code/fix-orientation-derivatives.sh | 92 +++++++++++++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 code/fix-orientation-derivatives.sh

diff --git a/code/fix-orientation-derivatives.sh b/code/fix-orientation-derivatives.sh
new file mode 100644
index 0000000000..2dbf857aa4
--- /dev/null
+++ b/code/fix-orientation-derivatives.sh
@@ -0,0 +1,92 @@
+#!/bin/bash
+#
+# Fixes orientation of derivatives labels
+#
+# Usage:
+#   ./process_data.sh <SUBJECT>
+#
+#
+# Authors: Sandrine Bédard
+# The following global variables are retrieved from the caller sct_run_batch
+# but could be overwritten by uncommenting the lines below:
+# PATH_DATA_PROCESSED="~/data_processed"
+# PATH_RESULTS="~/results"
+# PATH_LOG="~/log"
+# PATH_QC="~/qc"
+
+# Uncomment for full verbose
+set -x
+
+# Immediately exit if error
+set -e -o pipefail
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input params
+SUBJECT=$1
+# get starting time:
+start=`date +%s`
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+
+# Copy source images
+rsync -avzh $PATH_DATA/$SUBJECT .
+
+# Go to anat folder where all structural data are located
+cd ${SUBJECT}/anat/
+
+file_t2="${SUBJECT}_T2w"
+
+
+orient_native=`sct_image -i ${file_t2}.nii.gz -getorient | cut -f18 -d' '`
+orient_native=${orient_native:9:5}
+echo "Native orientation: $orient_native"
+
+
+
+# Copy CSF seg
+file_t2_csf="${file_t2}_label-CSF_seg"
+rsync -avzh $PATH_DATA/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz ${file_t2_csf}_or.nii.gz
+# Set to CSF seg to native orientation
+sct_image -i ${file_t2_csf}_or.nii.gz -setorient $orient_native -o ${file_t2_csf}_reorient.nii.gz
+
+
+# Resample no native resolution:
+
+sct_resample -i ${file_t2_csf}_reorient.nii.gz -ref ${file_t2}.nii.gz -x linear -o ${file_t2_csf}_reorient_r.nii.gz
+sct_maths -i ${file_t2_csf}_reorient_r.nii.gz -bin 0.5 -o ${file_t2_csf}_reorient_r_bin.nii.gz
+
+# Create QC report
+sct_qc -i ${file_t2}.nii.gz -s ${file_t2_csf}_reorient_r_bin.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
+
+# Create derivatives:
+mkdir -p $PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/
+rsync -avzh ${file_t2_csf}_reorient_r_bin.nii.gz $PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz
+
+
+# Verify presence of output files and write log file if error
+# ------------------------------------------------------------------------------
+FILES_TO_CHECK=(
+  "$PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz"
+)
+pwd
+for file in ${FILES_TO_CHECK[@]}; do
+  if [[ ! -e $file ]]; then
+    echo "${SUBJECT}/anat/${file} does not exist" >> $PATH_LOG/_error_check_output_files.log
+  fi
+done
+
+# Display useful info for the log
+end=`date +%s`
+runtime=$((end-start))
+echo
+echo "~~~"
+echo "SCT version: `sct_version`"
+echo "Ran on:      `uname -nsr`"
+echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+echo "~~~"

From f7f3db5827b7cc826588cbe8e78e768914f27303 Mon Sep 17 00:00:00 2001
From: Sandrine Bedard <sandrine.bedard@polymtl.ca>
Date: Mon, 5 Feb 2024 10:09:04 -0500
Subject: [PATCH 3/5] reorient and resample to native resolution

---
 .../anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz               | 2 +-
 .../sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz       | 2 +-
 .../sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz     | 2 +-
 .../sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz       | 2 +-
 .../sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz            | 2 +-
 .../anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz            | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
index 4b7c5136f2..0a50536fd7 100644
--- a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s54451--b9fceb6226f51439deb4469d51ffce2be3fe4a6d9bce35228ecf3e79179b89b5.nii.gz
+/annex/objects/SHA256E-s54564--81001a19991ea20a75d04a7144465d13503576dd6ce711ba59579000b98c47cc.nii.gz
diff --git a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
index 18b89e42a8..e48b21bd3e 100644
--- a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s50070--8f1dfbd634d0206c7df08467c50fba06fdbbbf0e35a17f5e271ee6b6a104d7c8.nii.gz
+/annex/objects/SHA256E-s50419--abb2afe982a1a2eefdf9942db37123120849674059dbf35219d24813e283d8eb.nii.gz
diff --git a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
index 05ce1e96ab..2f7c0c7b51 100644
--- a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s49620--481182b54b8f7b9c5b6a9cc939f949859310f1586962f61a8f60305c59290e27.nii.gz
+/annex/objects/SHA256E-s49939--21c50c9badcb46164f14f9abcd3a9ecff7f107a1407026f963117219ac9407f8.nii.gz
diff --git a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
index f26ffa5dc7..c18d3c0216 100644
--- a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s49132--ad01186cd1dec70a59ca848cc1e0415e44837c23324d18a81482146452fb6260.nii.gz
+/annex/objects/SHA256E-s49197--b7dfbf4e0feb6060455d4dd5cb3f6452e80163889475bac10b2bcc3e9a8cc72b.nii.gz
diff --git a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
index e791bd29a5..10de0c268f 100644
--- a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s51727--0674982ac05d6e6e64d2750e9d5bdc54115949332787a5de90f2e1b1f930d5ff.nii.gz
+/annex/objects/SHA256E-s51626--035ed29d77150800c009d1acc9b70364b2486f2f92dc78e49073dcbd6d985504.nii.gz
diff --git a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
index 696d8415b4..6201dcb3c8 100644
--- a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s46733--e52f42d538b043c6a2210074efbdcc81905e1e2f78305c0d86255f3a7b4be05b.nii.gz
+/annex/objects/SHA256E-s46991--e408ee4c0c38a56bd4f02801e96f55bef11ee10bfa9b130f9a2beb8771f45ce7.nii.gz
diff --git a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
index 876033db7e..fb1ff79357 100644
--- a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s48554--ff79d7209a9ee0283863ffebd0d9710568dea78aee36d0605f6444fb8d6f6306.nii.gz
+/annex/objects/SHA256E-s48522--298e436414af5fca0b20d18a261268b3b40756ae143d113204b6a9b0c93297cb.nii.gz
diff --git a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
index 8793f49cb3..d6712570b2 100644
--- a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s42478--573c05116cb4e6654e0ee1f5593b0e0aa4fcaa4f05d5260ea9116b0b1601a5fc.nii.gz
+/annex/objects/SHA256E-s42254--c8690f52a76400dd843cbdc57a00fc2db8c16df4484c2061bdaaa05871143fb5.nii.gz
diff --git a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
index e09cc34e85..4cb1e9a3ee 100644
--- a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s45727--88af42ae4b7def8c665a715bf6661d9f17f3190c833f3e7494e2fedcf7fd0c55.nii.gz
+/annex/objects/SHA256E-s45722--b3adbc6792fad44f5c23b797881a9a6731b0a4f210942acfe5c80e3bbb8f9b27.nii.gz
diff --git a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
index f4f54c254b..f957a03849 100644
--- a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s47804--9d59697a934d3e74cd20f891b8237c990cad8113860ec3459f55e661d6fd91df.nii.gz
+/annex/objects/SHA256E-s47790--ae4eed4ecb32f7ad1241038f5f3a436827c9aeffb6ee83a0a7be7de10f19e4d8.nii.gz

From 2cbfe7f06576c2747539acbaeef6a50fc50eaf31 Mon Sep 17 00:00:00 2001
From: Mathieu Guay-Paquet <mathieu.guay-paquet@polymtl.ca>
Date: Wed, 21 Feb 2024 16:55:37 -0500
Subject: [PATCH 4/5] Revert "reorient and resample to native resolution"

This reverts commit f7f3db5827b7cc826588cbe8e78e768914f27303.
---
 .../anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz               | 2 +-
 .../sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz       | 2 +-
 .../sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz     | 2 +-
 .../sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz       | 2 +-
 .../sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz   | 2 +-
 .../anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz            | 2 +-
 .../anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz            | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
index 0a50536fd7..4b7c5136f2 100644
--- a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s54564--81001a19991ea20a75d04a7144465d13503576dd6ce711ba59579000b98c47cc.nii.gz
+/annex/objects/SHA256E-s54451--b9fceb6226f51439deb4469d51ffce2be3fe4a6d9bce35228ecf3e79179b89b5.nii.gz
diff --git a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
index e48b21bd3e..18b89e42a8 100644
--- a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s50419--abb2afe982a1a2eefdf9942db37123120849674059dbf35219d24813e283d8eb.nii.gz
+/annex/objects/SHA256E-s50070--8f1dfbd634d0206c7df08467c50fba06fdbbbf0e35a17f5e271ee6b6a104d7c8.nii.gz
diff --git a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
index 2f7c0c7b51..05ce1e96ab 100644
--- a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s49939--21c50c9badcb46164f14f9abcd3a9ecff7f107a1407026f963117219ac9407f8.nii.gz
+/annex/objects/SHA256E-s49620--481182b54b8f7b9c5b6a9cc939f949859310f1586962f61a8f60305c59290e27.nii.gz
diff --git a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
index c18d3c0216..f26ffa5dc7 100644
--- a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s49197--b7dfbf4e0feb6060455d4dd5cb3f6452e80163889475bac10b2bcc3e9a8cc72b.nii.gz
+/annex/objects/SHA256E-s49132--ad01186cd1dec70a59ca848cc1e0415e44837c23324d18a81482146452fb6260.nii.gz
diff --git a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
index 10de0c268f..e791bd29a5 100644
--- a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s51626--035ed29d77150800c009d1acc9b70364b2486f2f92dc78e49073dcbd6d985504.nii.gz
+/annex/objects/SHA256E-s51727--0674982ac05d6e6e64d2750e9d5bdc54115949332787a5de90f2e1b1f930d5ff.nii.gz
diff --git a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
index 6201dcb3c8..696d8415b4 100644
--- a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s46991--e408ee4c0c38a56bd4f02801e96f55bef11ee10bfa9b130f9a2beb8771f45ce7.nii.gz
+/annex/objects/SHA256E-s46733--e52f42d538b043c6a2210074efbdcc81905e1e2f78305c0d86255f3a7b4be05b.nii.gz
diff --git a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
index fb1ff79357..876033db7e 100644
--- a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s48522--298e436414af5fca0b20d18a261268b3b40756ae143d113204b6a9b0c93297cb.nii.gz
+/annex/objects/SHA256E-s48554--ff79d7209a9ee0283863ffebd0d9710568dea78aee36d0605f6444fb8d6f6306.nii.gz
diff --git a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
index d6712570b2..8793f49cb3 100644
--- a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s42254--c8690f52a76400dd843cbdc57a00fc2db8c16df4484c2061bdaaa05871143fb5.nii.gz
+/annex/objects/SHA256E-s42478--573c05116cb4e6654e0ee1f5593b0e0aa4fcaa4f05d5260ea9116b0b1601a5fc.nii.gz
diff --git a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
index 4cb1e9a3ee..e09cc34e85 100644
--- a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s45722--b3adbc6792fad44f5c23b797881a9a6731b0a4f210942acfe5c80e3bbb8f9b27.nii.gz
+/annex/objects/SHA256E-s45727--88af42ae4b7def8c665a715bf6661d9f17f3190c833f3e7494e2fedcf7fd0c55.nii.gz
diff --git a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
index f957a03849..f4f54c254b 100644
--- a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
+++ b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz
@@ -1 +1 @@
-/annex/objects/SHA256E-s47790--ae4eed4ecb32f7ad1241038f5f3a436827c9aeffb6ee83a0a7be7de10f19e4d8.nii.gz
+/annex/objects/SHA256E-s47804--9d59697a934d3e74cd20f891b8237c990cad8113860ec3459f55e661d6fd91df.nii.gz

From 0d82233d2cfc7daa8fdb2f11a48bde676aed8b04 Mon Sep 17 00:00:00 2001
From: Mathieu Guay-Paquet <mathieu.guay-paquet@polymtl.ca>
Date: Wed, 21 Feb 2024 16:56:00 -0500
Subject: [PATCH 5/5] Revert "add code to fix csf orientation and pixdim to
 correspond with image native space"

This reverts commit 79e7157a149fe8a73af5d9f18ec3ccfad9ccc901.
---
 code/fix-orientation-derivatives.sh | 92 -----------------------------
 1 file changed, 92 deletions(-)
 delete mode 100644 code/fix-orientation-derivatives.sh

diff --git a/code/fix-orientation-derivatives.sh b/code/fix-orientation-derivatives.sh
deleted file mode 100644
index 2dbf857aa4..0000000000
--- a/code/fix-orientation-derivatives.sh
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/bin/bash
-#
-# Fixes orientation of derivatives labels
-#
-# Usage:
-#   ./process_data.sh <SUBJECT>
-#
-#
-# Authors: Sandrine Bédard
-# The following global variables are retrieved from the caller sct_run_batch
-# but could be overwritten by uncommenting the lines below:
-# PATH_DATA_PROCESSED="~/data_processed"
-# PATH_RESULTS="~/results"
-# PATH_LOG="~/log"
-# PATH_QC="~/qc"
-
-# Uncomment for full verbose
-set -x
-
-# Immediately exit if error
-set -e -o pipefail
-trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
-
-# Retrieve input params
-SUBJECT=$1
-# get starting time:
-start=`date +%s`
-
-# SCRIPT STARTS HERE
-# ==============================================================================
-# Display useful info for the log, such as SCT version, RAM and CPU cores available
-sct_check_dependencies -short
-
-# Go to folder where data will be copied and processed
-cd $PATH_DATA_PROCESSED
-
-# Copy source images
-rsync -avzh $PATH_DATA/$SUBJECT .
-
-# Go to anat folder where all structural data are located
-cd ${SUBJECT}/anat/
-
-file_t2="${SUBJECT}_T2w"
-
-
-orient_native=`sct_image -i ${file_t2}.nii.gz -getorient | cut -f18 -d' '`
-orient_native=${orient_native:9:5}
-echo "Native orientation: $orient_native"
-
-
-
-# Copy CSF seg
-file_t2_csf="${file_t2}_label-CSF_seg"
-rsync -avzh $PATH_DATA/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz ${file_t2_csf}_or.nii.gz
-# Set to CSF seg to native orientation
-sct_image -i ${file_t2_csf}_or.nii.gz -setorient $orient_native -o ${file_t2_csf}_reorient.nii.gz
-
-
-# Resample no native resolution:
-
-sct_resample -i ${file_t2_csf}_reorient.nii.gz -ref ${file_t2}.nii.gz -x linear -o ${file_t2_csf}_reorient_r.nii.gz
-sct_maths -i ${file_t2_csf}_reorient_r.nii.gz -bin 0.5 -o ${file_t2_csf}_reorient_r_bin.nii.gz
-
-# Create QC report
-sct_qc -i ${file_t2}.nii.gz -s ${file_t2_csf}_reorient_r_bin.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
-
-# Create derivatives:
-mkdir -p $PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/
-rsync -avzh ${file_t2_csf}_reorient_r_bin.nii.gz $PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz
-
-
-# Verify presence of output files and write log file if error
-# ------------------------------------------------------------------------------
-FILES_TO_CHECK=(
-  "$PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz"
-)
-pwd
-for file in ${FILES_TO_CHECK[@]}; do
-  if [[ ! -e $file ]]; then
-    echo "${SUBJECT}/anat/${file} does not exist" >> $PATH_LOG/_error_check_output_files.log
-  fi
-done
-
-# Display useful info for the log
-end=`date +%s`
-runtime=$((end-start))
-echo
-echo "~~~"
-echo "SCT version: `sct_version`"
-echo "Ran on:      `uname -nsr`"
-echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
-echo "~~~"