From 3931fdc3fdbb85e4d3c45250f82d1578c1e5411e Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Wed, 1 Jul 2026 14:14:36 -0700
Subject: [PATCH 01/29] remove APOE ref in spreadsheet unless it exists

---
 population_report.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/population_report.py b/population_report.py
index 696f1e6..6dcf18c 100644
--- a/population_report.py
+++ b/population_report.py
@@ -2297,9 +2297,12 @@ def get_case_stats(subject_id, timepoint):
 print('Report generated in ' + dir + '/reports/' + run_folder + '/population_report' + output_dir + "_" + date_filename + '.html')
 print('Excluded report generated in ' + dir + '/reports/' + run_folder + '/population_report_exclude' + output_dir + "_" + date_filename + '.html')
 
-if os.path.exists(os.path.join(dir, '../dce_available_3524_ac.xlsx')):
+apoe_file = os.path.join(dir, '../dce_available_3524_ac.xlsx')
+apoe_exists = os.path.exists(apoe_file)
+
+if apoe_exists:
     # add apoe and cdr fields to population_data
-    df = pd.read_excel(os.path.join(dir, '../dce_available_3524_ac.xlsx'), sheet_name="main")
+    df = pd.read_excel(apoe_file, sheet_name="main")
 
     # get apoe and cdr values for each subject
     for subject in population_data.keys():
@@ -2509,7 +2512,11 @@ def get_case_stats(subject_id, timepoint):
 df_success = pd.DataFrame(population_data)
 # df_exclude = pd.DataFrame(population_data_exclude)
 
-order = ["Date", "APOE", "Sex", "Age", "Machine", "Institution", "Coil", "TR", "Time_resolution", "TE", "Flip_angle", "n_reps",
+order = ["Date"]
+if apoe_exists:
+    order.append("APOE")
+order.extend([
+        "Sex", "Age", "Machine", "Institution", "Coil", "TR", "Time_resolution", "TE", "Flip_angle", "n_reps",
         "Approximate SNR", "AIFitness", "aif_fitted_r2", "manual_aif_status", "max_disp", "T1_blood", "T1_wm_median", "T1_gm_median",
         "Ktrans_wm_median", "Ktrans_gm_median", "Ktrans_Hippo_median", "Ktrans_PhG_median", "Ktrans_Putamen_median", "Ktrans_Pallidum_median",
         "Ktrans_Thalamus_median", "Ktrans_Caudate_median", "Ktrans_Amygdala_median", "Ktrans_Entorhinal_cortex_median",
@@ -2539,10 +2546,10 @@ def get_case_stats(subject_id, timepoint):
         "superiorparietal_thickness_avg", "superiorparietal_thickness_std", "superiortemporal_thickness_avg", "superiortemporal_thickness_std",
         "supramarginal_thickness_avg", "supramarginal_thickness_std", "frontalpole_thickness_avg", "frontalpole_thickness_std",
         "temporalpole_thickness_avg", "temporalpole_thickness_std", "transversetemporal_thickness_avg", "transversetemporal_thickness_std",
-        "insula_thickness_avg", "insula_thickness_std"]
+        "insula_thickness_avg", "insula_thickness_std"])
 
 df_success = df_success.T
-df_success = df_success[order]
+df_success = df_success.reindex(columns=order)
 
 
 order_exclude = order.copy()

From 488a33b307c3e06694243b666cf7b3e9bb9d4e25 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Wed, 1 Jul 2026 14:18:21 -0700
Subject: [PATCH 02/29] update refs to rawdata to fit new BIDS standard
 (v1.11.1)

rawdata is now sourcedata/raw, sometimes it's in the root but they don't make it clear when
---
 .github/workflows/DCE.yml | 4 ++--
 DCE_all.sh                | 2 +-
 README.md                 | 4 ++--
 preprocess_all.sh         | 5 +++--
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 3120896..eab42ab 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -53,10 +53,10 @@ jobs:
     #  uses: matlab-actions/setup-matlab@v1
         
     - name: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/rawdata -b -Z -m -c
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c
       
     - name: Run DCE
-      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/rawdata -f
+      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f
     
     - name: Output logs
       run:  |
diff --git a/DCE_all.sh b/DCE_all.sh
index aa540bf..a502201 100755
--- a/DCE_all.sh
+++ b/DCE_all.sh
@@ -35,7 +35,7 @@ while getopts ":d:C:fhl:sST:" options; do
 				DATA_DIR=${DATA_DIR::-1}
 			fi
 			date=$(date +%Y-%m-%d)
-			DERIV_DIR=$(dirname $DATA_DIR)/derivatives
+			DERIV_DIR=$(dirname $(dirname $DATA_DIR))/derivatives
 			LOG_FILE=$DERIV_DIR/logs/dce_log_$date.txt
 			if [ ! -d "$DATA_DIR/logs" ]
 				then
diff --git a/README.md b/README.md
index 1cb4bb8..60d3628 100644
--- a/README.md
+++ b/README.md
@@ -116,7 +116,7 @@ All data is assumed to be [BIDS](https://bids-specification.readthedocs.io/) com
 
 | Flag | Description |
 |---|---|
-| `-d [rawdata_path]` | **Required.** Path to your BIDS raw data folder. |
+| `-d [rawdata_path]` | **Required.** Path to your BIDS raw data (NIFTIs) folder. |
 | `-a [suffix]` | AIF suffix (default: `desc-AIF_mask`). `.nii.gz` is appended automatically. |
 | `-A [mode]` | Enable AutoAIF: `A` (fully automatic), `M` (manual if available), or `T` (manual + training if available). Requires the [vascular_function repo and weights](https://github.com/petmri/vascular_function). |
 | `-b` | Enable first round of bias field correction. |
@@ -216,7 +216,7 @@ All data is assumed to be [BIDS](https://bids-specification.readthedocs.io/) com
 
 | Flag | Description |
 |---|---|
-| `-d [path]` | **Required.** Path to raw BIDS data directory. |
+| `-d [path]` | **Required.** Path to raw BIDS data directory. Should be something like bids_root/sourcedata/raw |
 | `-C [name]` | Enable comparison mode. Copies essential files from a standard run if a preprocessed run of the same name does not exist. |
 | `-f` | Enable FreeSurfer WM parcellation for subregion analysis. |
 | `-s` | Skip cases already processed. |
diff --git a/preprocess_all.sh b/preprocess_all.sh
index 0195e70..c901fc1 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -71,8 +71,9 @@ while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:" options; do
 				DATA_DIR=${DATA_DIR::-1}
 			fi
 			DATE=$(date +%Y-%m-%d)
-			# derivatives dir is up 1 level from data dir
-			DERIV_DIR=$(dirname $DATA_DIR)/derivatives
+			# derivatives dir is up 2 levels from data dir
+			DERIV_DIR=$(dirname $(dirname $DATA_DIR))/derivatives
+			echo $DERIV_DIR
 			if [ ! -d "$DERIV_DIR" ]
 				then
 				mkdir -p "$DERIV_DIR"

From 17dbf22f0a59ad2902ae17f0bec26e67a0ca1d70 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Wed, 1 Jul 2026 15:12:11 -0700
Subject: [PATCH 03/29] do not double gaussian normalize a slice if there are
 too few WM voxels on that slice

---
 VFA_norm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VFA_norm.py b/VFA_norm.py
index 6896816..fab9b64 100644
--- a/VFA_norm.py
+++ b/VFA_norm.py
@@ -89,7 +89,7 @@ def double_gaussian(x, A1, mu1, sigma1, A2, mu2, sigma2):
             amp_guess = 0
             params = 0
             # check if slice is empty
-            if area == 0 or pstdev(wm_data[:,:,i][a]) == 0:
+            if area < 1000 or pstdev(wm_data[:,:,i][a]) == 0:
                 # just get from next slice
                 # if i == slice_num - 1:
                 #     a = np.where(wm_data[:,:,i-1] > 0)

From 3c343bb00112545c51ea86b53ca709a9c6549ab2 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Wed, 1 Jul 2026 15:22:12 -0700
Subject: [PATCH 04/29] update skip logic to look for gzipped T1map

---
 preprocess_all.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/preprocess_all.sh b/preprocess_all.sh
index c901fc1..0a700ea 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -283,7 +283,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	if [ $SKIP_IF_SUCCESS -eq 1 ]
 		then
 		if [ -f "dce/${PREFIX}_desc-bfcz_DCE.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_desc-brain_mask.nii.gz" ] && \
-			[ -f "dce/${PREFIX}_desc-AIF_T1map.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_T1map.nii" ] #&& [ -f "reports/${PREFIX}_desc-casereport.html" ]
+			[ -f "dce/${PREFIX}_desc-AIF_T1map.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_T1map.nii.gz" ] #&& [ -f "reports/${PREFIX}_desc-casereport.html" ]
 			then
 			echo "Skipping ${source_dir} because it has already been processed." >> $LOG_FILE
 			let successes++

From d3c8293bcb8bd1a39f22cfce718af386882ae470 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Fri, 21 Aug 2026 19:03:35 -0700
Subject: [PATCH 05/29] Refactor DCE and VFA processing scripts to use updated
 mask naming conventions

- Updated mask file naming from 'seg-WM_DCE.nii' to 'label-WM_DCE.nii' in DCE_norm.py.
- Adjusted file patterns and processing logic in VFA_norm.py to accommodate new mask naming.
- Modified case_report.py to reflect changes in mask file names and added a function for space-RAS path conversion.
- Updated ktrans_analysis.py to use 'label' prefixes for Ktrans files.
- Changed max_disp.py to dynamically display the total number of frames.
- Revised preprocess_all.sh to use 'label' suffixes for AIF masks and updated related file paths.
- Ensured consistency in mask handling across scripts, including brain and tissue masks.
- Updated documentation to reflect changes in file naming conventions for FreeSurfer parcellation.
---
 DCE_all.sh                             | 47 ++++++++------
 DCE_norm.py                            |  2 +-
 VFA_norm.py                            |  6 +-
 case_report.py                         | 72 +++++++++++++--------
 docs/how-to/freesurfer-parcellation.md |  2 +-
 ktrans_analysis.py                     |  6 +-
 max_disp.py                            |  2 +-
 preprocess_all.sh                      | 89 +++++++++++++++-----------
 8 files changed, 136 insertions(+), 90 deletions(-)

diff --git a/DCE_all.sh b/DCE_all.sh
index a502201..bf6a897 100755
--- a/DCE_all.sh
+++ b/DCE_all.sh
@@ -16,9 +16,10 @@ PURGE_INTERMEDIATES=0
 GIGA_PURGE=0
 TARGET_FLAG=0
 SCRIPT_LOOP_DIR=dceprep/sub-*/ses-*
+USE_PYTHON=0
 
 # options
-while getopts ":d:C:fhl:sST:" options; do
+while getopts ":d:C:fhl:sST:p" options; do
 	case "${options}" in
 		b)
 			EN_BIAS1=1
@@ -56,6 +57,7 @@ while getopts ":d:C:fhl:sST:" options; do
 			echo "-d: specify main data directory containing all subject folders"
 			echo "-f: enable Freesurfer wm parcellation for subregion analysis"
 			echo "-h: display this message"
+			echo "-p: use Python for ROCKETSHIP calls"
 			# echo "-l: specify a list of subjects to process (filename only, place in code folder)"
 			echo "-s: skip subjects that have already been processed"
 			echo "-S: enable smoothing of DCE input"
@@ -65,6 +67,9 @@ while getopts ":d:C:fhl:sST:" options; do
 		l)
 			INPUT_LIST=$DATA_DIR/../code/${OPTARG}
 			;;
+		p)
+			USE_PYTHON=1
+			;;
 		s)
 			SKIP_IF_SUCCESS=1
 			;;
@@ -194,9 +199,9 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 		cd $der_dir || echo "ERROR: $der_dir does not exist. Preprocess first or check the name and try again." >> $LOG_FILE
 	fi
 	SUBJECT_TP_PATH=$(pwd)
-	if [ ! -f anat/${PREFIX}_desc-brain_T1w.nii.gz ]
+	if [ ! -f anat/${PREFIX}_label-brain_T1w.nii.gz ]
 		then
-		cp -r $DERIV_DIR/dceprep-multihance_fix/$SUBJECT/$SESSION/anat/${PREFIX}_desc-brain_T1w.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/anat
+		cp -r $DERIV_DIR/dceprep-multihance_fix/$SUBJECT/$SESSION/anat/${PREFIX}_label-brain_T1w.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/anat
 	fi
 	# Locking mechanism to prevent concurrent processing from other machines
 	LOCKFILE="lock.txt"
@@ -249,8 +254,14 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	
 	# DCE
 	# ------------------------------
-	echo Begin DCE processing...
-	matlab -nodisplay -r "cd('$ROCKETSHIP_PATH'); addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; run_dce_cli('$DATA_DIR/$SUBJECT/$SESSION/', '$SUBJECT_TP_PATH/'); exit;"
+	# echo Begin DCE processing...
+	rm -f dce/dce_patlak_fit_rois.xls
+	if [ $USE_PYTHON -eq 1 ]
+		then
+		${ROCKETSHIP_PATH}/.venv/bin/python ${ROCKETSHIP_PATH}/run_dce_cli_python_case.py --subject-source $SUBJECT_TP_PATH --subject-tp $SUBJECT_TP_PATH --output-dir $SUBJECT_TP_PATH --events off
+	else
+		matlab -nodisplay -r "cd('$ROCKETSHIP_PATH'); addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; run_dce_cli('$DATA_DIR/$SUBJECT/$SESSION/', '$SUBJECT_TP_PATH/'); exit;"
+	fi
 	mv dce/dce_*_fit_Ktrans.nii dce/${PREFIX}_Ktrans.nii
 	mv dce/dce_*_fit_ktrans_ci_low.nii dce/${PREFIX}_Ktrans_ci_low.nii
 	mv dce/dce_*_fit_ktrans_ci_high.nii dce/${PREFIX}_Ktrans_ci_high.nii
@@ -278,25 +289,25 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	antsApplyTransforms -i anat/${PREFIX}_label-GM_mask.nii.gz -r $DCEREF_FILE -t anat/${PREFIX}_from-T1w_to-DCEref.mat -o anat/${PREFIX}_space-DCEref_label-GM_mask_pv.nii.gz &> /dev/null
 	fslmaths anat/${PREFIX}_space-DCEref_label-GM_mask_pv.nii.gz -thr 0.9 -bin anat/${PREFIX}_space-DCEref_label-GM_mask.nii.gz
 	rm anat/${PREFIX}_space-DCEref_label-GM_mask_pv.nii.gz
-	
+
 	# Align CSF mask
 	antsApplyTransforms -i anat/${PREFIX}_label-CSF_mask.nii.gz -r $DCEREF_FILE -t anat/${PREFIX}_from-T1w_to-DCEref.mat -o anat/${PREFIX}_space-DCEref_label-CSF_mask_pv.nii.gz &> /dev/null
 	fslmaths anat/${PREFIX}_space-DCEref_label-CSF_mask_pv.nii.gz -thr 0.9 -bin anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz
 	rm anat/${PREFIX}_space-DCEref_label-CSF_mask_pv.nii.gz
-	
+
 	# Apply masks to T1 map
 	fslmaths anat/${PREFIX}_space-DCEref_T1map.nii  -mas anat/${PREFIX}_space-DCEref_label-WM_mask.nii.gz anat/${PREFIX}_space-DCEref_label-WM_T1map.nii
 	fslmaths anat/${PREFIX}_space-DCEref_T1map.nii -mas anat/${PREFIX}_space-DCEref_label-GM_mask.nii.gz anat/${PREFIX}_space-DCEref_label-GM_T1map.nii
 	fslmaths anat/${PREFIX}_space-DCEref_T1map.nii -mas anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz anat/${PREFIX}_space-DCEref_label-CSF_T1map.nii
-	
+
 	# Apply masks to Ktrans map
-	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-WM_mask.nii.gz dce/${PREFIX}_seg-WM_Ktrans.nii
-	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-GM_mask.nii.gz dce/${PREFIX}_seg-GM_Ktrans.nii
-	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz dce/${PREFIX}_seg-CSF_Ktrans.nii
-	
+	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-WM_mask.nii.gz dce/${PREFIX}_label-WM_Ktrans.nii
+	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-GM_mask.nii.gz dce/${PREFIX}_label-GM_Ktrans.nii
+	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz dce/${PREFIX}_label-CSF_Ktrans.nii
+
 	# registration QC
 	python3 $SCRIPT_PATH/ktrans_analysis.py $dir $PREFIX
-	
+
 	fslmaths anat/${PREFIX}_space-DCEref_label-WM_mask.nii.gz -add 2000 huh.nii
 	fslmaths huh.nii.gz -thr 2001 huh.nii
 	fslmaths $DCEREF_FILE -sub huh.nii.gz bozo.nii
@@ -307,7 +318,6 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	fslmaths $DCEREF_FILE -sub huh2.nii.gz bozo2.nii
 	fslmaths bozo2.nii -thr 0 anat/${PREFIX}_space-DCEref_label-GMQC.nii.gz
 	rm huh.nii.gz huh2.nii.gz bozo.nii.gz bozo2.nii.gz
-		
 	# wm parcellation with Freesurfer
 	if [ $USE_FREESURFER -eq 1 ]
 		then
@@ -327,8 +337,8 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 			--o $DERIV_DIR/freesurfer/$SUBJECT/$SESSION/mri/wmparc-in-rawavg.mgz \
 			--regheader $DERIV_DIR/freesurfer/$SUBJECT/$SESSION/mri/wmparc.mgz &> /dev/null
         mri_convert $DERIV_DIR/freesurfer/$SUBJECT/$SESSION/mri/wmparc-in-rawavg.mgz wmparc.nii.gz &> /dev/null
-        antsApplyTransforms -i wmparc.nii.gz -r dce/${PREFIX}_desc-hmc_DCEref.nii.gz -t anat/${PREFIX}_from-t1w_to-DCEref.mat -n NearestNeighbor -o anat/${PREFIX}_space-DCEref_desc-wmparc.nii &> /dev/null
-        gzip -f anat/${PREFIX}_space-DCEref_desc-wmparc.nii &> /dev/null
+        antsApplyTransforms -i wmparc.nii.gz -r dce/${PREFIX}_desc-hmc_DCEref.nii.gz -t anat/${PREFIX}_from-t1w_to-DCEref.mat -n NearestNeighbor -o anat/${PREFIX}_space-DCEref_seg-wmparc_dseg.nii &> /dev/null
+        gzip -f anat/${PREFIX}_space-DCEref_seg-wmparc_dseg.nii &> /dev/null
 		rm wmparc.nii.gz
 	elif [ ! -f dce/${PREFIX}_space-MNI_Ktrans.nii.gz ]
 		then
@@ -339,8 +349,8 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 		# 	--winsorize-image-intensities [ 0.005,0.995 ] --transform Affine[ 0.1 ] \
 		# 	--metric MI[ T1_bet.nii.gz,DCE_mc.nii.gz,1,32,Regular,0.25 ] \
 		# 	--convergence [ 1000x500x250x100,1e-6,10 ] --shrink-factors 12x8x4x2 --smoothing-sigmas 4x3x2x1vox
-		# antsRegistrationSyNQuick.sh -d 3 -f anat/${PREFIX}_desc-brain_T1w.nii.gz -m dce/${PREFIX}_desc-hmc_DCEref.nii.gz -o dce/${PREFIX}_space-MNI_DCEref -n 8
-		antsRegistrationSyNQuick.sh -d 3 -f $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -m anat/${PREFIX}_desc-brain_T1w.nii.gz -o anat/${PREFIX}_space-MNI_T1w -n 8
+		# antsRegistrationSyNQuick.sh -d 3 -f anat/${PREFIX}_label-brain_T1w.nii.gz -m dce/${PREFIX}_desc-hmc_DCEref.nii.gz -o dce/${PREFIX}_space-MNI_DCEref -n 8
+		antsRegistrationSyNQuick.sh -d 3 -f $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -m anat/${PREFIX}_label-brain_T1w.nii.gz -o anat/${PREFIX}_space-MNI_T1w -n 8
 		# antsApplyTransforms -i dce/${PREFIX}_desc-hmc_DCEref.nii.gz -r $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -t dce/${PREFIX}_space-MNI_DCEref1Warp.nii.gz -t anat/${PREFIX}_space-MNI_T1w0GenericAffine.mat -t [ anat/${PREFIX}_from-T1w_to-DCEref.mat, 1] -o DCE_mc_MNI.nii.gz
 		antsApplyTransforms -i dce/${PREFIX}_desc-hmc_DCEref.nii.gz -r $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -t anat/${PREFIX}_space-MNI_T1w0GenericAffine.mat -t [ anat/${PREFIX}_from-T1w_to-DCEref.mat, 1] -o dce/${PREFIX}_space-MNI_DCEref.nii.gz
 		# antsRegistration --verbose 1 --dimensionality 3 --float 0 --collapse-output-transforms 1 \
@@ -358,6 +368,7 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	mkdir reports &> /dev/null
 	python3 $SCRIPT_PATH/case_report.py $DATA_DIR/$SUBJECT/$SESSION $PREFIX $USE_FREESURFER
 	python3 $SCRIPT_PATH/ktrans_report.py $DATA_DIR/$SUBJECT/$SESSION $PREFIX
+
 	if [ $PURGE_INTERMEDIATES -eq 1 ]
 		then
 		# rm -f !(Ktrans_*|T1_gm*|T1_wm*|T1_csf*|*_patlak_fit*.nii|case_report.html|*_MNI.nii.gz|*fit_VFA.nii|figures|dce*.png|*.log)
diff --git a/DCE_norm.py b/DCE_norm.py
index 163689e..14df0ae 100644
--- a/DCE_norm.py
+++ b/DCE_norm.py
@@ -202,7 +202,7 @@ def normalize(mri_file1, wm_masked, file_dir):   # THE FUNCTION PERFORMING THE N
     if str(file).endswith('desc-bfc_DCE.nii') or str(file).endswith('desc-bfc_DCE.nii.gz'):
         file1 = str(file)
         mask_file = file1.split('desc-bfc_DCE', 1)[0]
-        mask_file = mask_file + 'seg-WM_DCE.nii'
+        mask_file = mask_file + 'label-WM_DCE.nii'
 
         if Path(mask_file + ".gz").exists():
             mask_file += ".gz"
diff --git a/VFA_norm.py b/VFA_norm.py
index fab9b64..ef99b07 100644
--- a/VFA_norm.py
+++ b/VFA_norm.py
@@ -267,10 +267,10 @@ def double_gaussian(x, A1, mu1, sigma1, A2, mu2, sigma2):
     dir = Path(sys.argv[1])     # takes timepoint directory as argument
     prefix = sys.argv[2]
     BFC = sys.argv[3]
-    file_pattern = r'.*flip-\d+_space-DCEref_desc-bfc_VFA.nii.*' if BFC else r'.*flip-\d+_space-DCEref_desc-brain_VFA.nii.*'
+    file_pattern = r'.*flip-\d+_space-DCEref_desc-bfc_VFA.nii.*' if BFC else r'.*flip-\d+_space-DCEref_label-brain_VFA.nii.*'
     files_in_dir = dir.iterdir()
-    file_list = [file for file in files_in_dir if re.search(r'.*flip-\d+_space-DCEref_desc-brain_VFA.nii.*', str(file))]
+    file_list = [file for file in files_in_dir if re.search(r'.*flip-\d+_space-DCEref_label-brain_VFA.nii.*', str(file))]
     num_processes = len(file_list)
 
     with multiprocessing.Pool(processes=num_processes) as pool:
-        pool.starmap(normalize, [(str(file), str(file).split('_desc-brain', 1)[0] + '_seg-WM_VFA.nii.gz', str(dir)) for file in file_list])
+        pool.starmap(normalize, [(str(file), str(file).split('_label-brain', 1)[0] + '_label-WM_VFA.nii.gz', str(dir)) for file in file_list])
diff --git a/case_report.py b/case_report.py
index 62ef85f..6eb06d7 100644
--- a/case_report.py
+++ b/case_report.py
@@ -27,9 +27,32 @@
 
 files_to_reorient = [f'anat/{prefix}_flip-01_space-DCEref_VFA.nii.gz', f'dce/{prefix}_Ktrans.nii',
                      f'anat/{prefix}_space-DCEref_T1w.nii.gz', f'anat/{prefix}_space-DCEref_label-WM_mask.nii.gz',
-                     f'anat/{prefix}_space-DCEref_T1map.nii', f'anat/{prefix}_space-DCEref_desc-brain_mask.nii.gz',
-                     f'anat/{prefix}_space-DCEref_label-GM_mask.nii.gz', f'anat/{prefix}_space-DCEref_desc-wmparc.nii.gz',
+                     f'anat/{prefix}_space-DCEref_T1map.nii', f'anat/{prefix}_space-DCEref_label-brain_mask.nii.gz',
+                     f'anat/{prefix}_space-DCEref_label-GM_mask.nii.gz', f'anat/{prefix}_space-DCEref_seg-wmparc_dseg.nii.gz',
                      first_existing_nifti_path(f'dce/{prefix}_desc-hmc_DCEref.nii.gz', f'dce/{prefix}_DCEref.nii.gz')]
+
+
+def space_ras_path(path):
+    if path.endswith('.nii.gz'):
+        extension = '.nii.gz'
+        stem = path[:-7]
+    elif path.endswith('.nii'):
+        extension = '.nii'
+        stem = path[:-4]
+    else:
+        raise ValueError(f'Unsupported NIfTI path: {path}')
+
+    directory, filename = os.path.split(stem)
+    if 'space-DCEref_' in filename:
+        filename = filename.replace('space-DCEref_', 'space-RAS_', 1)
+    else:
+        filename, replacements = re.subn(r'(ses-[^_]+_)', r'\1space-RAS_', filename, count=1)
+        if replacements == 0:
+            raise ValueError(f'Could not derive space-RAS path from {path}')
+
+    return os.path.join(directory, filename + extension)
+
+
 # if c3d exists, reorient files to RAS
 dimensions = 0
 voxel_size = 0
@@ -42,12 +65,12 @@
         if not os.path.exists(file):
             print(f"File does not exist, skipping: {file}")
             continue
-        file_no_extension = nifti_stem(file)
-        command = ['c3d', file, '-orient', 'RAS', '-o', file_no_extension + '_RAS.nii.gz']
+        reoriented_file = space_ras_path(file)
+        command = ['c3d', file, '-orient', 'RAS', '-o', reoriented_file]
         try:
             subprocess.run(command, check=True)
             if nifti_stem(file) == f'dce/{prefix}_Ktrans':
-                ktrans = nib.load(resolve_nifti_path(f'dce/{prefix}_Ktrans_RAS.nii.gz'))
+                ktrans = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_Ktrans.nii')))
                 ktrans_data = ktrans.get_fdata()
                 ktrans_flipped = np.flip(ktrans_data, axis=1)
                 ktrans_flipped = nib.Nifti1Image(ktrans_flipped, ktrans.affine, ktrans.header)
@@ -75,12 +98,12 @@
         if not os.path.exists(file):
             print(f"File does not exist, skipping: {file}")
             continue
-        file_no_extension = nifti_stem(file)
-        command = ['mri_convert', '--in_orientation', 'LPI', file, file_no_extension + '_RAS.nii.gz']
+        reoriented_file = space_ras_path(file)
+        command = ['mri_convert', '--in_orientation', 'LPI', file, reoriented_file]
         try:
             subprocess.run(command, check=True)
             if nifti_stem(file) == f'dce/{prefix}_Ktrans':
-                ktrans = nib.load(resolve_nifti_path(f'dce/{prefix}_Ktrans_RAS.nii.gz'))
+                ktrans = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_Ktrans.nii')))
                 ktrans_data = ktrans.get_fdata()
                 ktrans_flipped = np.flip(ktrans_data, axis=1)
                 ktrans_flipped = nib.Nifti1Image(ktrans_flipped, ktrans.affine, ktrans.header)
@@ -158,7 +181,7 @@
 
 try:
     t1w_native = load_nifti_float32(f'{source_dir}/anat/{prefix}_T1w.nii.gz')
-    brain_mask_native = load_nifti_float32(f'anat/{prefix}_desc-brain_mask.nii.gz')
+    brain_mask_native = load_nifti_float32(f'anat/{prefix}_label-brain_mask.nii.gz')
     wm_mask_native = load_nifti_float32(f'anat/{prefix}_label-WM_mask.nii.gz')
     gm_mask_native = load_nifti_float32(f'anat/{prefix}_label-GM_mask.nii.gz')
 
@@ -175,33 +198,33 @@
 
 try:
     # T1w to VFA
-    # plotting.plot_anat(f'anat/{prefix}_label-WM_mask_RAS.nii.gz', cmap='gray', output_file='figures/t1w_to_dceref.svg', cut_coords=7, display_mode='z', annotate=False, colorbar=False, draw_cross=False, title='T1w to DCEref')
+    # plotting.plot_anat(space_ras_path(f'anat/{prefix}_label-WM_mask.nii.gz'), cmap='gray', output_file='figures/t1w_to_dceref.svg', cut_coords=7, display_mode='z', annotate=False, colorbar=False, draw_cross=False, title='T1w to DCEref')
 
     # T1w to dyn
-    t1w_dceref = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_T1w_RAS.nii.gz'))
+    t1w_dceref = nib.load(resolve_nifti_path(space_ras_path(f'anat/{prefix}_space-DCEref_T1w.nii.gz')))
     t1w_dceref_data = t1w_dceref.get_fdata()
     t1w_dceref_flipped = np.flip(t1w_dceref_data, axis=1)
     t1w_dceref_flipped = nib.Nifti1Image(t1w_dceref_flipped, t1w_dceref.affine, t1w_dceref.header)
     plotting.plot_anat(t1w_dceref_flipped, cmap='gray', output_file=f'figures/{prefix}_space-DCEref_T1w.svg', cut_coords=7, display_mode='z', annotate=False, colorbar=False, draw_cross=False, title='T1w to dyn')
 
     # flip T1w masks
-    t1w_mask = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_desc-brain_mask_RAS.nii.gz'))
+    t1w_mask = nib.load(resolve_nifti_path(space_ras_path(f'anat/{prefix}_space-DCEref_label-brain_mask.nii.gz')))
     t1w_mask_data = t1w_mask.get_fdata()
     t1w_mask_flipped = np.flip(t1w_mask_data, axis=1)
     t1w_mask_flipped = nib.Nifti1Image(t1w_mask_flipped, t1w_mask.affine, t1w_mask.header)
-    # nib.save(t1w_mask_flipped, str(tp_dir) + '/T1_bet_mask_RAS.nii')
+    # nib.save(t1w_mask_flipped, space_ras_path(str(tp_dir) + '/T1_bet_mask.nii'))
 
-    t1w_wm_mask = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_label-WM_mask_RAS.nii.gz'))
+    t1w_wm_mask = nib.load(resolve_nifti_path(space_ras_path(f'anat/{prefix}_space-DCEref_label-WM_mask.nii.gz')))
     t1w_wm_mask_data = t1w_wm_mask.get_fdata()
     t1w_wm_mask_flipped = np.flip(t1w_wm_mask_data, axis=1)
     t1w_wm_mask_flipped = nib.Nifti1Image(t1w_wm_mask_flipped, t1w_wm_mask.affine, t1w_wm_mask.header)
-    # nib.save(t1w_wm_mask_flipped, str(tp_dir) + '/T1_wm_mask_RAS.nii')
+    # nib.save(t1w_wm_mask_flipped, space_ras_path(str(tp_dir) + '/T1_wm_mask.nii'))
 
-    t1w_gm_mask = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_label-GM_mask_RAS.nii.gz'))
+    t1w_gm_mask = nib.load(resolve_nifti_path(space_ras_path(f'anat/{prefix}_space-DCEref_label-GM_mask.nii.gz')))
     t1w_gm_mask_data = t1w_gm_mask.get_fdata()
     t1w_gm_mask_flipped = np.flip(t1w_gm_mask_data, axis=1)
     t1w_gm_mask_flipped = nib.Nifti1Image(t1w_gm_mask_flipped, t1w_gm_mask.affine, t1w_gm_mask.header)
-    # nib.save(t1w_gm_mask_flipped, str(tp_dir) + '/T1_gm_mask_RAS.nii')
+    # nib.save(t1w_gm_mask_flipped, space_ras_path(str(tp_dir) + '/T1_gm_mask.nii'))
 
     plotting.plot_roi(t1w_mask_flipped, cmap='gray', bg_img=t1w_dceref_flipped, output_file='figures/t1bet_to_dyn.svg', display_mode='z', vmin=0, vmax=1, dim=0, annotate=True, colorbar=False, draw_cross=False, title='T1w brain mask to DCEref')
     plotting.plot_roi(t1w_wm_mask_flipped, cmap='gray', bg_img=t1w_dceref_flipped, output_file='figures/t1wm_to_dyn.svg', display_mode='z', vmin=0, vmax=1, dim=0, annotate=True, colorbar=False, draw_cross=False, title='T1w wm to DCEref')
@@ -277,7 +300,7 @@
 try:
     # T1 map
     # flip T1 map
-    img = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_T1map_RAS.nii.gz'))
+    img = nib.load(resolve_nifti_path(space_ras_path(f'anat/{prefix}_space-DCEref_T1map.nii.gz')))
     img_data = img.get_fdata()
     img_data = np.flip(img_data, axis=0)
     img_data = np.flip(img_data, axis=1)
@@ -289,8 +312,7 @@
 
 # try:
 # AIF
-# plot graph of AIF region
-aif = nib.load(resolve_nifti_path(f'dce/{prefix}_desc-AIFpos_T1map.nii.gz'))
+aif = nib.load(resolve_nifti_path(f'dce/{prefix}_label-AIF_T1map.nii.gz'))
 aif_data = aif.get_fdata()
 # img = nib.load(str(tp_dir) + '/DCE_mc.nii.gz')
 try:
@@ -353,15 +375,15 @@
 
 if freesurfer:
     # wmparc overlay on DCE
-    wmparc = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_desc-wmparc_RAS.nii.gz'))
+    wmparc = nib.load(resolve_nifti_path(space_ras_path(f'anat/{prefix}_space-DCEref_seg-wmparc_dseg.nii.gz')))
     wmparc_data = wmparc.get_fdata()
     wmparc_flipped = np.flip(wmparc_data, axis=1)
     wmparc_flipped = nib.Nifti1Image(wmparc_flipped, wmparc.affine, wmparc.header)
 
     try:
-        dce = nib.load(resolve_nifti_path(f'dce/{prefix}_desc-hmc_DCEref_RAS.nii.gz'))
+        dce = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_desc-hmc_DCEref.nii.gz')))
     except FileNotFoundError:
-        dce = nib.load(resolve_nifti_path(f'dce/{prefix}_DCEref_RAS.nii.gz'))
+        dce = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_DCEref.nii.gz')))
     dce_data = dce.get_fdata()
     dce_flipped = np.flip(dce_data, axis=1)
     dce_flipped = nib.Nifti1Image(dce_flipped, dce.affine, dce.header)
@@ -579,7 +601,7 @@ def extract_elapsed_time(log_text):
 # Ktrans
 
 # get Ktrans mean wm and gm
-ktrans_wm = nib.load(resolve_nifti_path(f'dce/{prefix}_seg-WM_Ktrans.nii.gz'))
+ktrans_wm = nib.load(resolve_nifti_path(f'dce/{prefix}_label-WM_Ktrans.nii.gz'))
 ktrans_wm_data = ktrans_wm.get_fdata()
 ktrans_wm_mask = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_label-WM_mask.nii.gz'))
 ktrans_wm_mask_data = ktrans_wm_mask.get_fdata()
@@ -587,7 +609,7 @@ def extract_elapsed_time(log_text):
 ktrans_median_wm = np.nanmedian(ktrans_wm_data[np.logical_and(ktrans_wm_mask_data > 0, ktrans_wm_data > KTRANS_MIN_THRESHOLD)])*1000
 ktrans_std_wm = np.nanstd(ktrans_wm_data[np.logical_and(ktrans_wm_mask_data > 0, ktrans_wm_data > KTRANS_MIN_THRESHOLD)])*1000
 
-ktrans_gm = nib.load(resolve_nifti_path(f'dce/{prefix}_seg-GM_Ktrans.nii.gz'))
+ktrans_gm = nib.load(resolve_nifti_path(f'dce/{prefix}_label-GM_Ktrans.nii.gz'))
 ktrans_gm_data = ktrans_gm.get_fdata()
 ktrans_gm_mask = nib.load(resolve_nifti_path(f'anat/{prefix}_space-DCEref_label-GM_mask.nii.gz'))
 ktrans_gm_mask_data = ktrans_gm_mask.get_fdata()
diff --git a/docs/how-to/freesurfer-parcellation.md b/docs/how-to/freesurfer-parcellation.md
index e956730..89b01d3 100644
--- a/docs/how-to/freesurfer-parcellation.md
+++ b/docs/how-to/freesurfer-parcellation.md
@@ -38,7 +38,7 @@ The registration pipeline:
 1. `mri_label2vol` converts `wmparc.mgz` from FreeSurfer conformed space to the subject's native T1w space (`rawavg`)
 2. `mri_convert` converts the result to NIfTI format
 3. `antsApplyTransforms` applies the T1w → DCE rigid transform (with nearest-neighbor interpolation) to bring the parcellation into DCE space
-4. The result is saved as `anat/sub-##_ses-##_space-DCEref_desc-wmparc.nii.gz`
+4. The result is saved as `anat/sub-##_ses-##_space-DCEref_seg-wmparc_dseg.nii.gz`
 
 ---
 
diff --git a/ktrans_analysis.py b/ktrans_analysis.py
index e388181..cc9abe7 100644
--- a/ktrans_analysis.py
+++ b/ktrans_analysis.py
@@ -19,9 +19,9 @@ def analyze(tp_dir):
     files = ['anat/' + prefix + '_space-DCEref_label-WM_T1map.nii.gz',
              'anat/' + prefix + '_space-DCEref_label-GM_T1map.nii.gz',
              'anat/' + prefix + '_space-DCEref_label-CSF_T1map.nii.gz',
-             'dce/' + prefix + '_seg-WM_Ktrans.nii.gz',
-             'dce/' + prefix + '_seg-GM_Ktrans.nii.gz',
-             'dce/' + prefix + '_seg-CSF_Ktrans.nii.gz',
+             'dce/' + prefix + '_label-WM_Ktrans.nii.gz',
+             'dce/' + prefix + '_label-GM_Ktrans.nii.gz',
+             'dce/' + prefix + '_label-CSF_Ktrans.nii.gz',
              'anat/' + prefix + '_space-DCEref_label-WM_mask.nii.gz',
              'anat/' + prefix + '_space-DCEref_label-GM_mask.nii.gz']
     # for i, file in enumerate(files):
diff --git a/max_disp.py b/max_disp.py
index c261928..6fe7be5 100644
--- a/max_disp.py
+++ b/max_disp.py
@@ -53,7 +53,7 @@
 plt.xlabel("")
 plt.ylim([-2.5, 2.5])
 plt.text(len(mc_params[:,0])/3, 2, "Max vector displacement: " + str(round(vector_max_disp,4)) + "mm")
-plt.text(len(mc_params[:,0])/3, 1.8, "Frame: " + str(vector_max_disp_i) + "/64")
+plt.text(len(mc_params[:,0])/3, 1.8, "Frame: " + str(vector_max_disp_i) + "/" + str(len(mc_params[:,0])))
 # plt.text(len(mc_params[:,0])/2, 1.8, "param: " + param_type)
 path = dir + '/../figures/displacements.svg'
 plt.savefig(path, bbox_inches='tight')
diff --git a/preprocess_all.sh b/preprocess_all.sh
index 0a700ea..e3d8901 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -9,8 +9,9 @@ EN_BIAS2=0
 EN_MOTION_CORR=0
 T1_ONLY=0
 USE_AUTO_AIF=0
-AIF_SUFFIX="desc-AIF_mask"
-AIF_TRAINING_SUFFIX="desc-trainingAIF_mask"
+USE_PYTHON=0
+AIF_SUFFIX="label-AIF_mask"
+AIF_TRAINING_SUFFIX="label-AIF_desc-training_mask"
 SKIP_IF_SUCCESS=0
 SCRIPT_LOOP_DIRS=sub-*/ses-*
 AUTOAIF_WEIGHT_PATH="docker/files/model_weight_huber1.h5"
@@ -90,7 +91,7 @@ while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:" options; do
 		h)
 			echo "This script runs through all subject folders of a specified main data directory, preprocessing every folder ending in '_timepoint'."
 			echo "The output is the DCE input, which are the corrected dynamic images, brain mask, T1 maps."
-			echo "-a: specify AIF suffix (default is 'desc-AIF_mask'). .nii.gz will be appended to the suffix."
+			echo "-a: specify AIF suffix (default is 'label-AIF_mask'). .nii.gz will be appended to the suffix."
 			echo "-A: enable AutoAIF with argument A (All automatic), M (Manual if available), or T (Manual + Training if available)"
 			echo "-b: enable first round of bias field corrections"
 			echo "-B: enable second round of bias field corrections, post-Z-norm if enabled"
@@ -103,6 +104,7 @@ while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:" options; do
 			echo "-T [dir_path]: target the subject(s)/session(s) to run (default is 'sub-*/ses-*/')"
 			echo "-t: only run up to T1 mapping"
 			echo "-w [path]: specify the path to the AutoAIF weights file"
+			echo "-p: Use Python for ROCKETSHIP calls"
 			echo "-Z: enable Z-slice normalization"
 			exit 0
 			;;
@@ -115,6 +117,9 @@ while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:" options; do
 		M)
 			AUTOAIF_MODEL=${OPTARG}
 			;;
+		p)
+			USE_PYTHON=1
+			;;
 		s)
 			SKIP_IF_SUCCESS=1
 			;;
@@ -228,11 +233,11 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 			# If the session string is not empty, copy the masks
 			if [ $mask_copied -eq 0 ] && [[ -n $session_str ]]; then
 				echo "Copying masks for $SUBJECT $SESSION..." >> $LOG_FILE
-				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/test/masks/sub-${pat}_ses-${session_num}_desc-AIF_mask.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
+				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/test/masks/sub-${pat}_ses-${session_num}_label-AIF_mask.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
 				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/test/masks/${pat}_${session_str}_timepoint.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
-				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/train/masks/sub-${pat}_ses-${session_num}_desc-AIF_mask.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
+				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/train/masks/sub-${pat}_ses-${session_num}_label-AIF_mask.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
 				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/train/masks/${pat}_${session_str}_timepoint.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
-				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/val/masks/sub-${pat}_ses-${session_num}_desc-AIF_mask.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
+				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/val/masks/sub-${pat}_ses-${session_num}_label-AIF_mask.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
 				cp /media/network_mriphysics/USC-PPG/AI_training/loos_model/val/masks/${pat}_${session_str}_timepoint.nii.gz $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${SUBJECT}_${SESSION}_${AIF_TRAINING_SUFFIX}.nii.gz && mask_copied=1
 			fi
 			if [ $mask_copied -eq 0 ] && [ ! -f $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${PREFIX}_${AIF_SUFFIX}.nii.gz ] && [ ! -f $DERIV_DIR/dceprep-$OUTPUT_DIR/$SUBJECT/$SESSION/dce/${PREFIX}_${AIF_TRAINING_SUFFIX}.nii.gz ] && [ $USE_AUTO_AIF -eq 2 ]
@@ -268,7 +273,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 		echo "$LOCKPATH" >> "$LOCKLIST"
 		trap 'for f in $(cat "$LOCKLIST" 2>/dev/null); do rm -f "$f"; done; rm -f "$LOCKLIST"; exit $?' INT TERM EXIT
 	else
-		echo "Skipping $dir because it is currently being processed by $(cat $LOCKPATH)." >> $LOG_FILE
+		echo "Skipping $source_dir because it is currently being processed by $(cat $LOCKPATH)." >> $LOG_FILE
 		cd $DERIV_DIR
 		continue
 	fi
@@ -282,8 +287,8 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 
 	if [ $SKIP_IF_SUCCESS -eq 1 ]
 		then
-		if [ -f "dce/${PREFIX}_desc-bfcz_DCE.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_desc-brain_mask.nii.gz" ] && \
-			[ -f "dce/${PREFIX}_desc-AIF_T1map.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_T1map.nii.gz" ] #&& [ -f "reports/${PREFIX}_desc-casereport.html" ]
+		if [ -f "dce/${PREFIX}_desc-bfcz_DCE.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_label-brain_mask.nii.gz" ] && \
+			[ -f "dce/${PREFIX}_label-AIF_T1map.nii.gz" ] && [ -f "anat/${PREFIX}_space-DCEref_T1map.nii.gz" ] #&& [ -f "reports/${PREFIX}_desc-casereport.html" ]
 			then
 			echo "Skipping ${source_dir} because it has already been processed." >> $LOG_FILE
 			let successes++
@@ -480,7 +485,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	if [ ! -f anat/${PREFIX}_label-WM_mask.nii.gz ]
 		then
 		echo -ne "T1 SEG w/ FAST [=>                                                ] $prog% ($current/$count) ~$mETA min remaining \r"
-		fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -b --nopve -g -o anat/${PREFIX}_label- anat/${PREFIX}_desc-brain_T1w.nii.gz
+		fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -b --nopve -g -o anat/${PREFIX}_label- anat/${PREFIX}_label-brain_T1w.nii.gz
 		# rename segmented files
 		mv anat/${PREFIX}_label-_bias.nii.gz anat/${PREFIX}_desc-bias_T1w.nii.gz
 		mv anat/${PREFIX}_label-_seg_0.nii.gz anat/${PREFIX}_label-CSF_mask.nii.gz
@@ -548,7 +553,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 		# apply MP-RAGE wm mask
 		for VFA in "${VFA_LIST[@]}"; do
 			# VFA_NUM=$(echo $VFA | grep -o '[0-9]*')
-			fslmaths anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-brain_VFA.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-WM_mask.nii.gz anat/${PREFIX}_${VFA}_${REF_SPACE}_seg-WM_VFA.nii.gz &> /dev/null
+			fslmaths anat/${PREFIX}_${VFA}_${REF_SPACE}_label-brain_VFA.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-WM_mask.nii.gz anat/${PREFIX}_${VFA}_${REF_SPACE}_label-WM_VFA.nii.gz &> /dev/null
 		done
 	fi
 
@@ -616,7 +621,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	else
 		echo Concatenating raw images
 		for VFA in "${VFA_DYN_LIST[@]}"; do
-			VFA_INPUT+="anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-brain_VFA.nii.gz "
+			VFA_INPUT+="anat/${PREFIX}_${VFA}_${REF_SPACE}_label-brain_VFA.nii.gz "
 		done
 		fslmerge -t anat/${PREFIX}_${REF_SPACE}_desc-unified_VFA.nii.gz $VFA_INPUT
 		VFA_INPUT="desc-unified_VFA"
@@ -671,9 +676,9 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	# -----------------------------	
 	prog=$(echo "scale=2;  $prog + 2.77 / $count" | bc -l)
 	echo -ne "REG BET MASK   [========================>                         ] $prog% ($current/$count) ~$ETA min remaining \r"
-	antsApplyTransforms -i anat/${PREFIX}_desc-brain_mask.nii.gz -r $DCE_REF_VOL -t $structural_to_DCEref -o anat/${PREFIX}_${REF_SPACE}_desc-brain_mask_pv.nii.gz &> /dev/null
-	fslmaths anat/${PREFIX}_${REF_SPACE}_desc-brain_mask_pv.nii.gz -thr 1 -bin anat/${PREFIX}_${REF_SPACE}_desc-brain_mask.nii.gz &> /dev/null
-	rm anat/${PREFIX}_${REF_SPACE}_desc-brain_mask_pv.nii.gz
+	antsApplyTransforms -i anat/${PREFIX}_label-brain_mask.nii.gz -r $DCE_REF_VOL -t $structural_to_DCEref -o anat/${PREFIX}_${REF_SPACE}_label-brain_desc-pv_mask.nii.gz &> /dev/null
+	fslmaths anat/${PREFIX}_${REF_SPACE}_label-brain_desc-pv_mask.nii.gz -thr 1 -bin anat/${PREFIX}_${REF_SPACE}_label-brain_mask.nii.gz &> /dev/null
+	rm anat/${PREFIX}_${REF_SPACE}_label-brain_desc-pv_mask.nii.gz
 	prog=$(echo "scale=2;  $prog + 0.55 / $count" | bc -l)
 	ETA=$(echo "scale=0;  $mETA - ($SECONDS)/60" | bc -l)
 	echo -ne "FAST DCE REP 1 [========================>                         ] $prog% ($current/$count) ~$ETA min remaining \r"
@@ -689,22 +694,29 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 				--model_name $AUTOAIF_MODEL \
 				--save_image 1 &> /dev/null
 			# rename output
-			mv dce/${PREFIX}_desc-hmc_DCE_float_mask.nii dce/${PREFIX}_desc-AIFfloat_mask.nii
-			mv dce/${PREFIX}_desc-hmc_DCE_mask.nii dce/${PREFIX}_desc-AIFtopvoxels_mask.nii
-			mv dce/${PREFIX}_desc-hmc_DCE_curve.svg figures/${PREFIX}_desc-AIF_resampledcurve.svg
-			mv dce/${PREFIX}_desc-hmc_DCE_mask.svg figures/${PREFIX}_desc-AIF_mask.svg
+			mv dce/${PREFIX}_desc-hmc_DCE_float_mask.nii dce/${PREFIX}_label-AIF_desc-float_mask.nii
+			mv dce/${PREFIX}_desc-hmc_DCE_mask.nii dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii
+			mv dce/${PREFIX}_desc-hmc_DCE_curve.svg figures/${PREFIX}_label-AIF_desc-resampled_mask.svg
+			mv dce/${PREFIX}_desc-hmc_DCE_mask.svg figures/${PREFIX}_label-AIF_mask.svg
 			# fslmaths aif_floats.nii -thr 0.95 aif_mask.nii
-			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_desc-AIFtopvoxels_mask.nii dce/${PREFIX}_desc-AIF_T1map.nii
+			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii dce/${PREFIX}_label-AIF_T1map.nii
 		else
 			python3 $AUTO_AIF_PATH/main_vif.py --mode inference --input_path $source_dir/dce/${PREFIX}_DCE.nii.gz --save_output_path $PWD/dce \
 				--model_weight_path $SCRIPT_PATH/$AUTOAIF_WEIGHT_PATH \
 				--model_name $AUTOAIF_MODEL \
-				--save_image 1 &> /dev/null
-			mv dce/${PREFIX}_DCE_float_mask.nii dce/${PREFIX}_AIFfloat_mask.nii
-			mv dce/${PREFIX}_DCE_mask.nii dce/${PREFIX}_AIFtopvoxels_mask.nii
-			mv dce/${PREFIX}_DCE_curve.svg figures/${PREFIX}_AIF_resampledcurve.svg
-			mv dce/${PREFIX}_DCE_mask.svg figures/${PREFIX}_AIF_mask.svg
-			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_AIFtopvoxels_mask.nii dce/${PREFIX}_desc-AIF_T1map.nii
+				--save_image 1 &> dce/${PREFIX}_desc-autoaif.log
+			if [ ! -f "dce/${PREFIX}_DCE_float_mask.nii" ] || [ ! -f "dce/${PREFIX}_DCE_mask.nii" ]; then
+				echo "$source_dir AutoAIF failed. See dce/${PREFIX}_desc-autoaif.log. Skipping timepoint..." >> "$LOG_FILE"
+				cd "$DATA_DIR"
+				fail=1
+				continue
+			fi
+			# rename output
+			mv dce/${PREFIX}_DCE_float_mask.nii dce/${PREFIX}_label-AIF_desc-float_mask.nii
+			mv dce/${PREFIX}_DCE_mask.nii dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii
+			mv dce/${PREFIX}_DCE_curve.svg figures/${PREFIX}_label-AIF_desc-resampled_mask.svg
+			mv dce/${PREFIX}_DCE_mask.svg figures/${PREFIX}_label-AIF_mask.svg
+			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii dce/${PREFIX}_label-AIF_T1map.nii
 		fi
 	elif [ $USE_AUTO_AIF -eq 2 ]
 		then
@@ -712,29 +724,30 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 		if [ -f "dce/${PREFIX}_${AIF_SUFFIX}.nii.gz" ]
 			then
 			# use manual AIF
-			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_${AIF_SUFFIX}.nii.gz dce/${PREFIX}_desc-AIF_T1map.nii.gz
+			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_${AIF_SUFFIX}.nii.gz dce/${PREFIX}_label-AIF_T1map.nii.gz
 		elif [ -f "dce/${PREFIX}_${AIF_TRAINING_SUFFIX}.nii.gz" ]
 			then
 			# use training manual AIF
-			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_${AIF_TRAINING_SUFFIX}.nii.gz dce/${PREFIX}_desc-AIF_T1map.nii.gz
+			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_${AIF_TRAINING_SUFFIX}.nii.gz dce/${PREFIX}_label-AIF_T1map.nii.gz
 		fi
 	else
 		# use manual AIF
-		fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_${AIF_SUFFIX}.nii.gz dce/${PREFIX}_desc-AIF_T1map.nii.gz
+		fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_${AIF_SUFFIX}.nii.gz dce/${PREFIX}_label-AIF_T1map.nii.gz
 	fi
 	# ensure AIF is included in mask
 	# fslcpgeom 2.nii T1_bet_mask_dyn.nii.gz
-	cp dce/${PREFIX}_desc-AIF_T1map.nii.gz dce/${PREFIX}_desc-AIFaligned_T1map.nii.gz
-	fslcpgeom anat/${PREFIX}_${REF_SPACE}_desc-brain_mask.nii.gz dce/${PREFIX}_desc-AIFaligned_T1map.nii
-	fslmaths dce/${PREFIX}_desc-AIFaligned_T1map.nii.gz -thr 0 dce/${PREFIX}_desc-AIFpos_T1map.nii &> /dev/null
-	rm dce/${PREFIX}_desc-AIFaligned_T1map.nii.gz
-	fslmaths anat/${PREFIX}_${REF_SPACE}_desc-brain_mask.nii.gz -add dce/${PREFIX}_desc-AIFpos_T1map.nii -thr 1 -bin anat/${PREFIX}_${REF_SPACE}_desc-brainAIF_mask.nii.gz &> /dev/null
+	cp dce/${PREFIX}_label-AIF_T1map.nii.gz dce/${PREFIX}_label-AIF_desc-aligned_T1map.nii.gz
+	fslcpgeom anat/${PREFIX}_${REF_SPACE}_label-brain_mask.nii.gz dce/${PREFIX}_label-AIF_desc-aligned_T1map.nii
+	fslmaths dce/${PREFIX}_label-AIF_desc-aligned_T1map.nii.gz -thr 0 dce/${PREFIX}_label-AIF_desc-pos_T1map.nii &> /dev/null
+	rm dce/${PREFIX}_label-AIF_desc-aligned_T1map.nii.gz
+	fslmaths anat/${PREFIX}_${REF_SPACE}_label-brain_mask.nii.gz -add dce/${PREFIX}_label-AIF_desc-pos_T1map.nii -thr 1 -bin anat/${PREFIX}_${REF_SPACE}_label-brainAIF_mask.nii.gz &> /dev/null
+	rm dce/${PREFIX}_label-AIF_desc-pos_T1map.nii
 	# apply AIF mask to all DCE images
 	if [ $EN_MOTION_CORR -eq 1 ]
 		then
-		fslmaths dce/${PREFIX}_desc-hmc_DCE.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_desc-brainAIF_mask.nii.gz dce/${PREFIX}_desc-AIFincluded_DCE.nii.gz &> /dev/null
+		fslmaths dce/${PREFIX}_desc-hmc_DCE.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-brainAIF_mask.nii.gz dce/${PREFIX}_desc-AIFincluded_DCE.nii.gz &> /dev/null
 	else
-		fslmaths $source_dir/dce/${PREFIX}_DCE.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_desc-brainAIF_mask.nii.gz dce/${PREFIX}_desc-AIFincluded_DCE.nii.gz &> /dev/null
+		fslmaths $source_dir/dce/${PREFIX}_DCE.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-brainAIF_mask.nii.gz dce/${PREFIX}_desc-AIFincluded_DCE.nii.gz &> /dev/null
 	fi
 	if [ $EN_BIAS1 -eq 1 ]
 		then
@@ -814,9 +827,9 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	# apply wm mask to all DCE images
 	if [ $EN_BIAS1 -eq 1 ]
 		then
-		fslmaths dce/${PREFIX}_desc-bfc_DCE.nii.gz -mas anat/${PREFIX}_${VFA}_${REF_SPACE}_seg-WM_VFA.nii.gz dce/${PREFIX}_seg-WM_DCE.nii.gz &> /dev/null
+		fslmaths dce/${PREFIX}_desc-bfc_DCE.nii.gz -mas anat/${PREFIX}_${VFA}_${REF_SPACE}_label-WM_VFA.nii.gz dce/${PREFIX}_label-WM_DCE.nii.gz &> /dev/null
 	else
-		fslmaths $source_dir/dce/${PREFIX}_DCE.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-WM_mask.nii.gz dce/${PREFIX}_seg-WM_DCE.nii.gz &> /dev/null
+		fslmaths $source_dir/dce/${PREFIX}_DCE.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-WM_mask.nii.gz dce/${PREFIX}_label-WM_DCE.nii.gz &> /dev/null
 	fi
 
 	# normalize dynamic images

From 769459deb15df08459e1a60875f343a3737e2a93 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Fri, 21 Aug 2026 19:06:45 -0700
Subject: [PATCH 06/29] Add support for Python execution in T1 mapping process

---
 preprocess_all.sh | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/preprocess_all.sh b/preprocess_all.sh
index e3d8901..f83855d 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -641,10 +641,15 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	
 	# T1 mapping where the input image is 'VFA.nii'
 	# ------------------------------
-	matlab -nodisplay -r "cd('$ROCKETSHIP_PATH/parametric_scripts/custom_scripts'); addpath '$ROCKETSHIP_PATH'; \
-		addpath '$ROCKETSHIP_PATH/dce'; addpath '$ROCKETSHIP_PATH/external_programs'; \
-		addpath '$ROCKETSHIP_PATH/external_programs/niftitools'; addpath '$ROCKETSHIP_PATH/parametric_scripts';	\
-		addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; T1mapping_fit('$source_dir/anat', '$SUBJECT_TP_PATH/anat', '${PREFIX}_${REF_SPACE}_${VFA_INPUT}.nii'); exit;" &> /dev/null
+	if [ $USE_PYTHON -eq 1 ]
+		then
+		${ROCKETSHIP_PATH}/.venv/bin/python ${ROCKETSHIP_PATH}/run_parametric_python_case.py --subject-source $source_dir --subject-tp $SUBJECT_TP_PATH --output-dir $SUBJECT_TP_PATH --events off
+	else
+		matlab -nodisplay -r "cd('$ROCKETSHIP_PATH/parametric_scripts/custom_scripts'); addpath '$ROCKETSHIP_PATH'; \
+			addpath '$ROCKETSHIP_PATH/dce'; addpath '$ROCKETSHIP_PATH/external_programs'; \
+			addpath '$ROCKETSHIP_PATH/external_programs/niftitools'; addpath '$ROCKETSHIP_PATH/parametric_scripts';	\
+			addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; T1mapping_fit('$source_dir/anat', '$SUBJECT_TP_PATH/anat', '${PREFIX}_${REF_SPACE}_${VFA_INPUT}.nii'); exit;"
+	fi
 	[ -f "anat/T1_map_t1_fa_fit_${PREFIX}_${REF_SPACE}_${VFA_INPUT}.nii" ] && mv anat/T1_map_t1_fa_fit_${PREFIX}_${REF_SPACE}_${VFA_INPUT}.nii anat/${PREFIX}_${REF_SPACE}_T1map.nii
 	[ -f "anat/T1_map_t1_fa_fit_${PREFIX}_${REF_SPACE}_${VFA_INPUT}.mat" ] && mv anat/T1_map_t1_fa_fit_${PREFIX}_${REF_SPACE}_${VFA_INPUT}.mat anat/${PREFIX}_${REF_SPACE}_T1map.mat
 	[ -f "anat/T1_map_t1_fa_fit_${PREFIX}_${REF_SPACE}_${VFA_INPUT}.txt" ] && mv anat/T1_map_t1_fa_fit_${PREFIX}_${REF_SPACE}_${VFA_INPUT}.txt anat/${PREFIX}_${REF_SPACE}_T1map.txt

From 49a483bd198fec7fef170fd43b55d8d54df9e798 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Fri, 21 Aug 2026 19:10:16 -0700
Subject: [PATCH 07/29] Add Python job to actions

---
 .github/workflows/DCE.yml | 75 ++++++++++++++++++++++++++++++++++++---
 1 file changed, 71 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index eab42ab..876ab93 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -10,7 +10,7 @@ permissions:
   contents: read
 
 jobs:
-  run:
+  run_case_matlab:
 
     runs-on: self-hosted
 
@@ -36,8 +36,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade hd-bet
     #    pip install flake8 pytest
-        
-        
+
    # - name: Lint with flake8
    #   run: |
    #     # stop the build if there are Python syntax errors or undefined names
@@ -79,8 +78,76 @@ jobs:
         retention-days: 7
         if-no-files-found: error
 
+  run_case_python:
+
+    runs-on: self-hosted
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v6
+
+    - name: Checkout ROCKETSHIP repo
+      uses: actions/checkout@v6
+      with:
+        repository: petmri/ROCKETSHIP
+        ref: dev
+        path: ROCKETSHIP
+
+    #- name: Set up Python 3.10
+    #  uses: actions/setup-python@v3
+    #  with:
+    #    python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install --upgrade hd-bet
+    #    pip install flake8 pytest
+
+   # - name: Lint with flake8
+   #   run: |
+   #     # stop the build if there are Python syntax errors or undefined names
+   #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+   #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+   #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    #- name: Test with pytest
+    #  run: |
+    #    pytest
+
+    #- name: Set up MATLAB
+    #  uses: matlab-actions/setup-matlab@v1
+        
+    - name: Preprocess the data
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p
+      
+    - name: Run DCE
+      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f -p
+    
+    - name: Output logs
+      run:  |
+        date=$(date +"%Y-%m-%d")
+        cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/preprocessing_log_${date}.txt
+        cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/dce_log_${date}.txt
+
+    - name: Convert HTML to PDF
+      run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+      continue-on-error: true
+
+    - name: Upload analysis results
+      uses: actions/upload-artifact@v7
+      with:
+        name: HTML_report
+        path: |
+          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
+          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/
+        retention-days: 7
+        if-no-files-found: error
+
   docker:
-    needs: run
+    needs: run_case_matlab
     strategy:
       fail-fast: false
       matrix:

From 32e0495c69f2f07c1a677d02d7c3c89ac8b3233f Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Fri, 21 Aug 2026 19:35:05 -0700
Subject: [PATCH 08/29] add p to getopts list

---
 preprocess_all.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/preprocess_all.sh b/preprocess_all.sh
index f83855d..8c98cfd 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -29,7 +29,7 @@ prog=0
 successes=0
 
 # options
-while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:" options; do
+while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:p" options; do
 	case "${options}" in
 		a)
 			AIF_SUFFIX=${OPTARG}

From 3ee50b83e67d922440d1bbf2ac171d9fcffcfe6c Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Mon, 24 Aug 2026 13:10:58 -0700
Subject: [PATCH 09/29] genericizing a couple calls for env var compat, add
 ability to limit parallel jobs,  new path search method, log autoAIF

---
 preprocess_all.sh | 89 ++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 77 insertions(+), 12 deletions(-)

diff --git a/preprocess_all.sh b/preprocess_all.sh
index 8c98cfd..e0e5de7 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -16,6 +16,9 @@ SKIP_IF_SUCCESS=0
 SCRIPT_LOOP_DIRS=sub-*/ses-*
 AUTOAIF_WEIGHT_PATH="docker/files/model_weight_huber1.h5"
 AUTOAIF_MODEL="best"
+HD_BET_COMMAND="${HD_BET_COMMAND:-hd-bet}"
+AUTO_AIF_PYTHON="${AUTO_AIF_PYTHON:-python3}"
+MAX_PARALLEL_JOBS=0
 
 # internal vars (don't change)
 fail=0
@@ -29,7 +32,7 @@ prog=0
 successes=0
 
 # options
-while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:p" options; do
+while getopts ":d:bBa:A:ZfhcC:j:mMsS:tl:T:w:p" options; do
 	case "${options}" in
 		a)
 			AIF_SUFFIX=${OPTARG}
@@ -99,6 +102,7 @@ while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:p" options; do
 			echo "-C [name]: enable comparison mode, which will output all files to the specified directory within each timepoint"
 			echo "-d [dir_path]: specify BIDS compliant data directory containing all subject folders (sub-*/ses-*/anat|dce/*.nii|*.json)"
 			echo "-h: display this message"
+			echo "-j [count]: limit concurrent VFA registration and FAST jobs (default is unlimited)"
 			echo "-m: enable motion correction"
 			echo "-s: skip preprocessing if DCE input file already exists"
 			echo "-T [dir_path]: target the subject(s)/session(s) to run (default is 'sub-*/ses-*/')"
@@ -111,6 +115,13 @@ while getopts ":d:bBa:A:ZfhcC:mMsS:tl:T:w:p" options; do
 		l)
 			INPUT_LIST=$DATA_DIR/../code/${OPTARG}
 			;;
+		j)
+			if [[ ! "$OPTARG" =~ ^[1-9][0-9]*$ ]]; then
+				echo "Invalid argument for -j. Use a positive integer."
+				exit 1
+			fi
+			MAX_PARALLEL_JOBS=$OPTARG
+			;;
 		m)
 			EN_MOTION_CORR=1
 			;;
@@ -148,16 +159,64 @@ if [ -z "$DATA_DIR" ]
 		exit 1
 fi
 
+if ! "$HD_BET_COMMAND" --help &> /dev/null; then
+	echo "ERROR: HD-BET command '$HD_BET_COMMAND' is unavailable or cannot start. Set HD_BET_COMMAND to a working hd-bet executable." >&2
+	exit 1
+fi
+
+resolve_tool_path() {
+	local configured_path=$1
+	local marker_file=$2
+	shift 2
+	local candidate_path
+
+	if [ -n "$configured_path" ]; then
+		if [ -f "$configured_path/$marker_file" ]; then
+			printf '%s\n' "$configured_path"
+			return 0
+		fi
+		echo "ERROR: Configured path $configured_path does not contain $marker_file." >&2
+		return 1
+	fi
+
+	for candidate_path in "$@"; do
+		if [ -f "$candidate_path/$marker_file" ]; then
+			printf '%s\n' "$candidate_path"
+			return 0
+		fi
+	done
+
+	find "$HOME" \
+		\( -path "$HOME/.local/share/Trash" -o -path "$HOME/.local/share/Trash/*" -o -path "$HOME/.Trash" -o -path "$HOME/.Trash/*" \) -prune -o \
+		-type f -name "$marker_file" -printf '%h\n' -quit 2> /dev/null
+}
+
 if [[ "$OSTYPE" == "linux-gnu" ]]; then
-	ROCKETSHIP_PATH=$(find $HOME -name '*run_dce_cli.m' -printf '%h\n' -quit || find / -name '*run_dce_cli.m' -printf '%h\n' -quit) &> /dev/null
+	ROCKETSHIP_PATH=$(resolve_tool_path "${ROCKETSHIP_PATH:-}" "run_dce_cli.m" "/opt/ROCKETSHIP/ROCKETSHIP-dev")
 	SCRIPT_PATH=$(dirname "$(realpath $0)")
-	GPUFIT_PATH=$(find $HOME -name 'GpufitCudaAvailableMex.mexa64' -printf '%h\n' -quit || find / -name 'GpufitCudaAvailableMex.mexa64' -printf '%h\n' -quit) &> /dev/null
-	GPUFIT_M_PATH=$(find $HOME -name 'ModelID.m' -printf '%h\n' -quit || find / -name 'ModelID.m' -printf '%h\n' -quit) &> /dev/null
+	GPUFIT_PATH=$(resolve_tool_path "${GPUFIT_PATH:-}" "GpufitCudaAvailableMex.mexa64" "/opt/Gpufit/matlab64")
+	GPUFIT_M_PATH=$(resolve_tool_path "${GPUFIT_M_PATH:-}" "ModelID.m" "/opt/Gpufit/matlab")
+	if [ -z "$ROCKETSHIP_PATH" ] || [ -z "$GPUFIT_PATH" ] || [ -z "$GPUFIT_M_PATH" ]; then
+		echo "ERROR: Unable to locate ROCKETSHIP or GPUfit. Set ROCKETSHIP_PATH, GPUFIT_PATH, and GPUFIT_M_PATH to directories containing their required MATLAB files." >&2
+		exit 1
+	fi
 else
 	ROCKETSHIP_PATH=$(find $HOME -type d -name ROCKETSHIP)
 	SCRIPT_PATH=$(find $HOME -type d -name in-house_toolbox)
 	GPUFIT_PATH=$(find $HOME -type d -name Gpufit-build)
 fi
+
+if [ $USE_AUTO_AIF -eq 1 ]; then
+	AUTO_AIF_PATH=$(resolve_tool_path "${AUTO_AIF_PATH:-}" "main_vif.py" "/opt/vascular_function")
+	if [ -z "$AUTO_AIF_PATH" ]; then
+		echo "ERROR: Unable to locate AutoAIF. Set AUTO_AIF_PATH to the directory containing main_vif.py." >&2
+		exit 1
+	fi
+	if ! "$AUTO_AIF_PYTHON" -c 'import tensorflow' &> /dev/null; then
+		echo "ERROR: AutoAIF Python '$AUTO_AIF_PYTHON' cannot import TensorFlow. Set AUTO_AIF_PYTHON to a TensorFlow-capable interpreter." >&2
+		exit 1
+	fi
+fi
 cd $DATA_DIR || exit 1
 
 # count timepoints
@@ -337,7 +396,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 	SECONDS=0
 	echo -ne "HD-BET MP-RAGE [                                                  ] $prog% ($current/$count) Calculating runtime...   \r"
 
-	if [ ! -f "anat/${PREFIX}_desc-brain_mask.nii.gz" ] && [ -f "$source_dir/anat/${PREFIX}_T1w.nii.gz" ]
+	if [ ! -f "anat/${PREFIX}_label-brain_mask.nii.gz" ] && [ -f "$source_dir/anat/${PREFIX}_T1w.nii.gz" ]
 		then
 		if [ nvidia-smi ]
 			then
@@ -505,7 +564,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 		# VFA_NUM=$(echo $VFA | grep -o '[0-9]*')
 		# FAST documentation recommends brain masking first
 		# fslmaths $VFA -mas T1_bet_mask.nii.gz ${VFA_NUM}_masked.nii
-		cp anat/${PREFIX}_${VFA}_${REF_SPACE}_VFA.nii.gz anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-brain_VFA.nii.gz
+		cp anat/${PREFIX}_${VFA}_${REF_SPACE}_VFA.nii.gz anat/${PREFIX}_${VFA}_${REF_SPACE}_label-brain_VFA.nii.gz
 	done
 	# gzip -f *_masked.nii
 
@@ -514,15 +573,15 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 			VFA_FAST () {
 				local VFA=$1
 				# VFA_NUM=$(echo $VFA | grep -o '[0-9]*')
-				fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -B --nopve -o anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-brain_VFA.nii.gz
+				fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -B --nopve -o anat/${PREFIX}_${VFA}_${REF_SPACE}_label-brain_VFA.nii.gz
 				# ETA=$(echo "scale=0;  $mETA - ($SECONDS)/60" | bc -l)
 				# prog=$(echo "scale=2;  $prog + 6 / $count" | bc -l)
 				# echo -ne "BFC FAST VFA${VFA_NUM}  [=======>                                          ] $prog% ($current/$count) ~$ETA min remaining \r"
-				mv anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-brain_VFA_restore* anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-bfc_VFA.nii.gz
+				mv anat/${PREFIX}_${VFA}_${REF_SPACE}_label-brain_VFA_restore* anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-bfc_VFA.nii.gz
 				# rm ${VFA}_masked_[mps]*
 
 				# apply wm mask to all VFAs
-				fslmaths anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-bfc_VFA.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-WM_mask.nii.gz anat/${PREFIX}_${VFA}_${REF_SPACE}_seg-WM_VFA.nii.gz
+				fslmaths anat/${PREFIX}_${VFA}_${REF_SPACE}_desc-bfc_VFA.nii.gz -mas anat/${PREFIX}_${REF_SPACE}_label-WM_mask.nii.gz anat/${PREFIX}_${VFA}_${REF_SPACE}_label-WM_VFA.nii.gz
 			}
 
 			#echo "Bias field correction with FAST"
@@ -694,10 +753,16 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 		# run AutoAIF
 		if [ $EN_MOTION_CORR -eq 1 ]
 			then
-			python3 $AUTO_AIF_PATH/main_vif.py --mode inference --input_path dce/${PREFIX}_desc-hmc_DCE.nii.gz --save_output_path $PWD/dce \
+			"$AUTO_AIF_PYTHON" $AUTO_AIF_PATH/main_vif.py --mode inference --input_path dce/${PREFIX}_desc-hmc_DCE.nii.gz --save_output_path $PWD/dce \
 				--model_weight_path $SCRIPT_PATH/$AUTOAIF_WEIGHT_PATH \
 				--model_name $AUTOAIF_MODEL \
-				--save_image 1 &> /dev/null
+				--save_image 1 &> dce/${PREFIX}_desc-autoaif.log
+			if [ ! -f "dce/${PREFIX}_desc-hmc_DCE_float_mask.nii" ] || [ ! -f "dce/${PREFIX}_desc-hmc_DCE_mask.nii" ]; then
+				echo "$source_dir AutoAIF failed. See dce/${PREFIX}_desc-autoaif.log. Skipping timepoint..." >> "$LOG_FILE"
+				cd "$DATA_DIR"
+				fail=1
+				continue
+			fi
 			# rename output
 			mv dce/${PREFIX}_desc-hmc_DCE_float_mask.nii dce/${PREFIX}_label-AIF_desc-float_mask.nii
 			mv dce/${PREFIX}_desc-hmc_DCE_mask.nii dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii
@@ -706,7 +771,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 			# fslmaths aif_floats.nii -thr 0.95 aif_mask.nii
 			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii dce/${PREFIX}_label-AIF_T1map.nii
 		else
-			python3 $AUTO_AIF_PATH/main_vif.py --mode inference --input_path $source_dir/dce/${PREFIX}_DCE.nii.gz --save_output_path $PWD/dce \
+			"$AUTO_AIF_PYTHON" $AUTO_AIF_PATH/main_vif.py --mode inference --input_path $source_dir/dce/${PREFIX}_DCE.nii.gz --save_output_path $PWD/dce \
 				--model_weight_path $SCRIPT_PATH/$AUTOAIF_WEIGHT_PATH \
 				--model_name $AUTOAIF_MODEL \
 				--save_image 1 &> dce/${PREFIX}_desc-autoaif.log

From 97ebacf09a0f3e3d350bf119a4ab437165da3b3f Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Mon, 24 Aug 2026 13:50:42 -0700
Subject: [PATCH 10/29] idk how autoAIF wasn't enabled in runner

---
 .github/workflows/DCE.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 876ab93..6000476 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -52,7 +52,7 @@ jobs:
     #  uses: matlab-actions/setup-matlab@v1
         
     - name: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -A A
       
     - name: Run DCE
       run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f
@@ -120,7 +120,7 @@ jobs:
     #  uses: matlab-actions/setup-matlab@v1
         
     - name: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p -A A
       
     - name: Run DCE
       run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f -p

From df27f4695b3c55aebd51f4383d76468cc37153e9 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Mon, 24 Aug 2026 14:40:35 -0700
Subject: [PATCH 11/29] update checkout actions

---
 .github/workflows/DCE.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 6000476..9df2062 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -16,10 +16,10 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Checkout ROCKETSHIP repo
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
       with:
         repository: petmri/ROCKETSHIP
         ref: dev
@@ -84,10 +84,10 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Checkout ROCKETSHIP repo
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
       with:
         repository: petmri/ROCKETSHIP
         ref: dev
@@ -156,7 +156,7 @@ jobs:
     runs-on: self-hosted
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     
     - name: Extract branch name
       id: extract_branch

From f82bae69366a6b5ff17b26bedea8fb3cf6056a7b Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Mon, 24 Aug 2026 18:57:11 -0700
Subject: [PATCH 12/29] stupid runner not updating repo

---
 .github/workflows/DCE.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 9df2062..71bf1b4 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -17,6 +17,9 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
+      with:
+        clean: true
+        fetch-depth: 0
 
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
@@ -24,6 +27,8 @@ jobs:
         repository: petmri/ROCKETSHIP
         ref: dev
         path: ROCKETSHIP
+        clean: true
+        fetch-depth: 0
 
     #- name: Set up Python 3.10
     #  uses: actions/setup-python@v3

From 8baf94a9db20aaf3332881830b89b314be1bd105 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Mon, 24 Aug 2026 19:06:04 -0700
Subject: [PATCH 13/29] surely this is the last line i need

---
 .github/workflows/DCE.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 71bf1b4..ce499d0 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -18,6 +18,7 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v7
       with:
+        ref: ${{ github.ref_name }}
         clean: true
         fetch-depth: 0
 

From af3f0516d531a59875710dd5b3355bf20ec82836 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Mon, 24 Aug 2026 19:06:55 -0700
Subject: [PATCH 14/29] forgot it for python run LUL

---
 .github/workflows/DCE.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index ce499d0..b4da801 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -91,6 +91,10 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
+      with:
+        ref: ${{ github.ref_name }}
+        clean: true
+        fetch-depth: 0
 
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7

From 2611b69ee7f7282c8fde65a916a6fd15dfbc6388 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 25 Aug 2026 17:57:45 +0000
Subject: [PATCH 15/29] Fix PR checkout ref handling

Co-authored-by: lsaca05 <46550669+lsaca05@users.noreply.github.com>
---
 .github/workflows/DCE.yml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index b4da801..e7d7bb1 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -17,11 +17,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
-      with:
-        ref: ${{ github.ref_name }}
-        clean: true
-        fetch-depth: 0
-
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
       with:
@@ -91,11 +86,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
-      with:
-        ref: ${{ github.ref_name }}
-        clean: true
-        fetch-depth: 0
-
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
       with:

From 36178cc68af6460bf7bc339dd7546db02047dec5 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 25 Aug 2026 18:16:07 +0000
Subject: [PATCH 16/29] Run workflow on all branches

Co-authored-by: lsaca05 <46550669+lsaca05@users.noreply.github.com>
---
 .github/workflows/DCE.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index e7d7bb1..c96e68e 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -2,9 +2,7 @@ name: Run DCE then build docker
 
 on:
   push:
-    branches: [ "dev", "main" ]
   pull_request:
-    branches: [ "dev", "main" ]
 
 permissions:
   contents: read
@@ -12,6 +10,7 @@ permissions:
 jobs:
   run_case_matlab:
 
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
     runs-on: self-hosted
 
     steps:
@@ -81,6 +80,7 @@ jobs:
 
   run_case_python:
 
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
     runs-on: self-hosted
 
     steps:

From 59d249167d2c5eac264ed492696499c3d15966ee Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 25 Aug 2026 11:25:14 -0700
Subject: [PATCH 17/29] another attempt at getting PRs to pull the right thing

---
 .github/workflows/DCE.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index c96e68e..3b378d4 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -16,6 +16,11 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
+      with:
+        repository: ${{ github.event.pull_request.head.repo.full_name }}
+        ref: ${{ github.event.pull_request.head.sha }}
+        fetch-depth: 0
+
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
       with:
@@ -86,6 +91,11 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
+      with:
+        repository: ${{ github.event.pull_request.head.repo.full_name }}
+        ref: ${{ github.event.pull_request.head.sha }}
+        fetch-depth: 0
+
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
       with:

From 4d8ad7697e5a6a0344586c923b6a115607f6fdce Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 25 Aug 2026 11:48:04 -0700
Subject: [PATCH 18/29] turns out me just dumb

---
 preprocess_all.sh | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/preprocess_all.sh b/preprocess_all.sh
index e0e5de7..9edf313 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -398,16 +398,22 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 
 	if [ ! -f "anat/${PREFIX}_label-brain_mask.nii.gz" ] && [ -f "$source_dir/anat/${PREFIX}_T1w.nii.gz" ]
 		then
-		if [ nvidia-smi ]
+		if command -v nvidia-smi &> /dev/null && nvidia-smi &> /dev/null
 			then
-			hd-bet -i $source_dir/anat/${PREFIX}_T1w.nii.gz -o anat/${PREFIX}_desc-brain.nii.gz --save_bet_mask &> /dev/null
+			"$HD_BET_COMMAND" -i $source_dir/anat/${PREFIX}_T1w.nii.gz -o anat/${PREFIX}_label-brain.nii.gz --save_bet_mask &> /dev/null
 			mETA=$(echo "scale=0;  $SECONDS * 34 * ($count - $current + 1) / 60" | bc -l)
 		else
-			hd-bet -i $source_dir/anat/${PREFIX}_T1w.nii.gz -o anat/${PREFIX}_desc-brain.nii.gz -device cpu --save_bet_mask &> /dev/null
+			"$HD_BET_COMMAND" -i $source_dir/anat/${PREFIX}_T1w.nii.gz -o anat/${PREFIX}_label-brain.nii.gz -device cpu --save_bet_mask &> /dev/null
 			mETA=$(echo "scale=0;  $SECONDS * 2 * ($count - $current + 1) / 60" | bc -l)
 		fi
-		mv anat/${PREFIX}_desc-brain_bet.nii.gz anat/${PREFIX}_desc-brain_mask.nii.gz
-		mv anat/${PREFIX}_desc-brain.nii.gz anat/${PREFIX}_desc-brain_T1w.nii.gz
+		if [ ! -f "anat/${PREFIX}_label-brain_bet.nii.gz" ] || [ ! -f "anat/${PREFIX}_label-brain.nii.gz" ]; then
+			echo "$source_dir HD-BET did not create expected output files. Skipping timepoint..." >> "$LOG_FILE"
+			cd "$DATA_DIR"
+			fail=1
+			continue
+		fi
+		mv anat/${PREFIX}_label-brain_bet.nii.gz anat/${PREFIX}_label-brain_mask.nii.gz
+		mv anat/${PREFIX}_label-brain.nii.gz anat/${PREFIX}_label-brain_T1w.nii.gz
 	elif [ -f "$source_dir/anat/${PREFIX}_T2w.nii.gz" ]
 		then
 		# assume mouse

From 60450cf45383b75a86582854e17fec204347cf71 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 25 Aug 2026 12:43:06 -0700
Subject: [PATCH 19/29] revert checkout specifying, only do docker on the core
 branches

---
 .github/workflows/DCE.yml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 3b378d4..2dd2bdc 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -16,10 +16,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
-      with:
-        repository: ${{ github.event.pull_request.head.repo.full_name }}
-        ref: ${{ github.event.pull_request.head.sha }}
-        fetch-depth: 0
 
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
@@ -91,10 +87,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v7
-      with:
-        repository: ${{ github.event.pull_request.head.repo.full_name }}
-        ref: ${{ github.event.pull_request.head.sha }}
-        fetch-depth: 0
 
     - name: Checkout ROCKETSHIP repo
       uses: actions/checkout@v7
@@ -158,6 +150,7 @@ jobs:
 
   docker:
     needs: run_case_matlab
+    if: github.ref == 'refs/heads/dev' || github.ref == 'refs/heads/main'
     strategy:
       fail-fast: false
       matrix:

From ccf00edd8d1f8c585f0d606142c30ad2a6aa7754 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 25 Aug 2026 13:22:01 -0700
Subject: [PATCH 20/29] fail actions if any result files are missing

---
 .github/workflows/DCE.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 2dd2bdc..8b4b929 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -68,6 +68,12 @@ jobs:
       run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
       continue-on-error: true
 
+    - name: Validate analysis results
+      run: |
+        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
+        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+        test -n "$(find /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/ -type f -print -quit)"
+
     - name: Upload analysis results
       uses: actions/upload-artifact@v7
       with:
@@ -137,6 +143,12 @@ jobs:
       run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
       continue-on-error: true
 
+    - name: Validate analysis results
+      run: |
+        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
+        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+        test -n "$(find /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/ -type f -print -quit)"
+
     - name: Upload analysis results
       uses: actions/upload-artifact@v7
       with:

From 73a4c94c64cfd3705ca792afc5f4fd4e515b08f4 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 25 Aug 2026 14:09:25 -0700
Subject: [PATCH 21/29] use new env for to specify workspace ROCKETSHIP

---
 .github/workflows/DCE.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 8b4b929..3ccdb53 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -12,6 +12,8 @@ jobs:
 
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
     runs-on: self-hosted
+    env:
+      ROCKETSHIP_PATH: ${{ github.workspace }}/ROCKETSHIP
 
     steps:
     - name: Checkout
@@ -89,6 +91,8 @@ jobs:
 
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
     runs-on: self-hosted
+    env:
+      ROCKETSHIP_PATH: ${{ github.workspace }}/ROCKETSHIP
 
     steps:
     - name: Checkout

From e12c6f8c28f0942b2f10603fa34d2a58ebd31be0 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 25 Aug 2026 14:52:08 -0700
Subject: [PATCH 22/29] Refactor DCEPrep integration scripts to use environment
 variables for ROCKETSHIP and GPUFIT paths, streamline preprocessing, and
 update documentation for clarity.

---
 .github/workflows/DCE.yml             | 48 +++++----------------------
 DCE_all.sh                            | 11 +++---
 docs/integration/gpufit.md            | 17 ++++------
 docs/integration/rocketship.md        |  6 ++--
 docs/integration/vascular-function.md | 15 +++++++--
 docs/reference/preprocessing-cli.md   |  8 +++++
 docs/user-guide/outputs.md            |  2 +-
 preprocess_all.sh                     |  1 -
 8 files changed, 45 insertions(+), 63 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 3ccdb53..5571bab 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -28,32 +28,16 @@ jobs:
         clean: true
         fetch-depth: 0
 
-    #- name: Set up Python 3.10
-    #  uses: actions/setup-python@v3
-    #  with:
-    #    python-version: "3.10"
+    - name: Set up ROCKETSHIP venv
+      working-directory: ROCKETSHIP
+      run: python3 install.py -G -M
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade hd-bet
-    #    pip install flake8 pytest
-
-   # - name: Lint with flake8
-   #   run: |
-   #     # stop the build if there are Python syntax errors or undefined names
-   #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-   #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-   #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    #- name: Test with pytest
-    #  run: |
-    #    pytest
-
-    #- name: Set up MATLAB
-    #  uses: matlab-actions/setup-matlab@v1
-        
+
     - name: Preprocess the data
       run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -A A
       
@@ -105,32 +89,16 @@ jobs:
         ref: dev
         path: ROCKETSHIP
 
-    #- name: Set up Python 3.10
-    #  uses: actions/setup-python@v3
-    #  with:
-    #    python-version: "3.10"
+    - name: Set up ROCKETSHIP venv
+      working-directory: ROCKETSHIP
+      run: python3 install.py -G -M
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade hd-bet
-    #    pip install flake8 pytest
-
-   # - name: Lint with flake8
-   #   run: |
-   #     # stop the build if there are Python syntax errors or undefined names
-   #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-   #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-   #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    #- name: Test with pytest
-    #  run: |
-    #    pytest
-
-    #- name: Set up MATLAB
-    #  uses: matlab-actions/setup-matlab@v1
-        
+
     - name: Preprocess the data
       run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p -A A
       
diff --git a/DCE_all.sh b/DCE_all.sh
index bf6a897..2e73045 100755
--- a/DCE_all.sh
+++ b/DCE_all.sh
@@ -99,10 +99,11 @@ if [ -z "$DATA_DIR" ]
 		exit 1
 fi
 if [[ "$OSTYPE" == "linux-gnu" ]]; then
-	ROCKETSHIP_PATH=$(find $HOME -name '*run_dce_cli.m' -printf '%h\n' -quit || find / -name '*run_dce_cli.m' -printf '%h\n' -quit) &> /dev/null
+	# respect a pre-set path (e.g. from CI) instead of searching the whole filesystem
+	ROCKETSHIP_PATH=${ROCKETSHIP_PATH:-$(find $HOME -name '*run_dce_cli.m' -printf '%h\n' -quit || find / -name '*run_dce_cli.m' -printf '%h\n' -quit) 2> /dev/null}
 	SCRIPT_PATH=$(dirname "$(realpath $0)")
-	GPUFIT_PATH=$(find $HOME -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit || find / -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit)
-	GPUFIT_M_PATH=$(find $HOME -name 'ModelID.m' -printf '%h\n' -quit || find / -name 'ModelID.m' -printf '%h\n' -quit)
+	GPUFIT_PATH=${GPUFIT_PATH:-$(find $HOME -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit || find / -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit)}
+	GPUFIT_M_PATH=${GPUFIT_M_PATH:-$(find $HOME -name 'ModelID.m' -printf '%h\n' -quit || find / -name 'ModelID.m' -printf '%h\n' -quit)}
 else
 	ROCKETSHIP_PATH=$(find $HOME -type d -name ROCKETSHIP)
 	SCRIPT_PATH=$(find $HOME -type d -name in-house_toolbox)
@@ -223,14 +224,14 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	fi
 	if [ $SKIP_IF_SUCCESS -eq 1 ]
 		then
-		if [ -f "reports/${PREFIX}_desc-casereport.html" ] && [ -f "anat/${PREFIX}_space-DCEref_desc-wmparc.nii.gz" ]
+		if [ -f "reports/${PREFIX}_desc-casereport.html" ] && [ -f "anat/${PREFIX}_space-DCEref_seg-wmparc_dseg.nii.gz" ]
 			then
 			echo "Skipping $dir because it has already been processed." >> $LOG_FILE
 			((successes++))
 			if [ $PURGE_INTERMEDIATES -eq 1 ] # && [ $COMPARISON_MODE -eq 1 ]
 				then
 				cd anat
-				rm -f !(${PREFIX}*bfczunified_VFA.nii|${PREFIX}_space-DCEref_T1map*|${PREFIX}*label-*_T1map*|*.mat|*wmparc.nii.gz|*space-DCEref_desc-brain_mask.nii.gz)
+				rm -f !(${PREFIX}*bfczunified_VFA.nii|${PREFIX}_space-DCEref_T1map*|${PREFIX}*label-*_T1map*|*.mat|*wmparc.nii.gz|*space-DCEref_label-brain_mask.nii.gz)
 				cd ../dce
 				rm -f !(${PREFIX}*Ktrans*|${PREFIX}*bfcz_DCE*|${PREFIX}*AIFincluded*|${PREFIX}*AIF_T1map*|figures|*.log|*.txt|*.par)
 			fi
diff --git a/docs/integration/gpufit.md b/docs/integration/gpufit.md
index 4623ee5..e28c46a 100644
--- a/docs/integration/gpufit.md
+++ b/docs/integration/gpufit.md
@@ -34,19 +34,14 @@ GPUfit (petmri fork) includes GPU-optimised implementations of:
 
 ## How DCEPrep Locates GPUfit
 
-DCEPrep searches for GPUfit's MEX files and MATLAB model definitions at startup:
+On Linux, `preprocess_all.sh` first uses `GPUFIT_PATH` and `GPUFIT_M_PATH` when
+set, then the Docker locations `/opt/Gpufit/matlab64` and `/opt/Gpufit/matlab`,
+and finally searches `$HOME` for the required files. Set both variables for a
+nonstandard installation:
 
 ```bash
-# T1 mapping MEX (preprocess_all.sh)
-GPUFIT_PATH=$(find $HOME -name 'GpufitCudaAvailableMex.mexa64' -printf '%h\n' -quit \
-  || find / -name 'GpufitCudaAvailableMex.mexa64' -printf '%h\n' -quit)
-
-# DCE analysis MEX (DCE_all.sh)
-GPUFIT_PATH=$(find $HOME -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit \
-  || find / -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit)
-
-# MATLAB model ID definitions (both scripts)
-GPUFIT_M_PATH=$(find $HOME -name 'ModelID.m' -printf '%h\n' -quit)
+export GPUFIT_PATH=/path/to/Gpufit/matlab64
+export GPUFIT_M_PATH=/path/to/Gpufit/matlab
 ```
 
 Both `GPUFIT_PATH` and `GPUFIT_M_PATH` are then passed to MATLAB via `addpath`:
diff --git a/docs/integration/rocketship.md b/docs/integration/rocketship.md
index 5c3e6d2..b2acfa8 100644
--- a/docs/integration/rocketship.md
+++ b/docs/integration/rocketship.md
@@ -15,10 +15,12 @@ DCEPrep uses [ROCKETSHIP](https://github.com/petmri/ROCKETSHIP) (version 1.2+),
 
 ## How DCEPrep Locates ROCKETSHIP
 
-DCEPrep finds the ROCKETSHIP installation at runtime by searching for `run_dce_cli.m`:
+On Linux, `preprocess_all.sh` first uses `ROCKETSHIP_PATH` when set, then the
+Docker location `/opt/ROCKETSHIP/ROCKETSHIP-dev`, and finally searches `$HOME`
+for `run_dce_cli.m`. Set the variable explicitly for a nonstandard installation:
 
 ```bash
-find / -name '*run_dce_cli.m' 2>/dev/null
+export ROCKETSHIP_PATH=/path/to/ROCKETSHIP
 ```
 
 In Docker, ROCKETSHIP is installed at a fixed path and the script preferences are mounted at:
diff --git a/docs/integration/vascular-function.md b/docs/integration/vascular-function.md
index cb43386..54ac557 100644
--- a/docs/integration/vascular-function.md
+++ b/docs/integration/vascular-function.md
@@ -33,11 +33,20 @@ vascular_function produces the following files per subject:
 
 ## How DCEPrep Locates vascular_function
 
-At runtime DCEPrep searches for `main_vif.py`:
+For automatic AIF selection, `preprocess_all.sh` first uses `AUTO_AIF_PATH`
+when set, then the Docker location `/opt/vascular_function`, and finally
+searches `$HOME` for `main_vif.py`. Set the variable explicitly for a
+nonstandard installation:
 
 ```bash
-AUTO_AIF_PATH=$(find $HOME -wholename '*main_vif.py' -printf '%h\n' -quit \
-  || find / -name '*main_vif.py' -printf '%h\n' -quit)
+export AUTO_AIF_PATH=/path/to/vascular_function
+```
+
+`main_vif.py` requires TensorFlow. `preprocess_all.sh` uses `python3` by default;
+set `AUTO_AIF_PYTHON` when TensorFlow is installed in a dedicated environment:
+
+```bash
+export AUTO_AIF_PYTHON=/path/to/tensorflow-environment/bin/python
 ```
 
 In Docker, vascular_function is installed at `/opt/vascular_function` and the pre-trained model weights are mounted at:
diff --git a/docs/reference/preprocessing-cli.md b/docs/reference/preprocessing-cli.md
index 9f95000..bc7fec2 100644
--- a/docs/reference/preprocessing-cli.md
+++ b/docs/reference/preprocessing-cli.md
@@ -21,6 +21,7 @@ Full reference for `preprocess_all.sh`.
 | `-B` | — | No | Enable **second round** of bias field correction (applied after z-normalization). Only relevant when `-Z` is also set. |
 | `-c` | — | No | Clean the case's derivatives folder before processing. Ensures a fresh run; disables skip behavior. |
 | `-C` | `name` | No | Enable [comparison mode](../how-to/comparison-mode.md). Writes outputs to `derivatives/sub-##/ses-##/<name>/`. |
+| `-j` | `count` | No | Limit concurrent VFA registration and FAST jobs. Defaults to unlimited to preserve existing behavior. Start with `2` when running multiple cases on one host. |
 | `-m` | — | No | Enable head motion correction using FSL `mcflirt`. |
 | `-s` | — | No | Skip preprocessing if the final DCE output file already exists. |
 | `-t` | — | No | Run only up to T1 map generation (skip DCE processing). Useful for T1-only protocols. |
@@ -28,6 +29,13 @@ Full reference for `preprocess_all.sh`.
 | `-w` | `path` | No | Path to the AutoAIF neural network weights file. |
 | `-Z` | — | No | Enable z-axis slice normalization on VFA and DCE images. |
 
+### Environment variables
+
+| Variable | Description |
+|---|---|
+| `HD_BET_COMMAND` | HD-BET executable to use. Defaults to `hd-bet`; set it when the default launcher is not associated with a working HD-BET environment. |
+| `AUTO_AIF_PYTHON` | Python interpreter for AutoAIF. Defaults to `python3` and must be able to import TensorFlow when `-A A` is used. |
+
 ---
 
 ## Example Invocations
diff --git a/docs/user-guide/outputs.md b/docs/user-guide/outputs.md
index 75a0454..9af8b11 100644
--- a/docs/user-guide/outputs.md
+++ b/docs/user-guide/outputs.md
@@ -134,7 +134,7 @@ The spreadsheet contains the following column groups:
 | **Demographics** | Date, APOE, Sex, Age |
 | **Scanner** | Machine, Institution, Coil |
 | **Acquisition** | TR, Time_resolution, TE, Flip_angle, n_reps |
-| **QC** | Approximate SNR, AIFitness, aif_fitted_r2, manual_aif_status, max_disp |
+| **QC** | Approximate_SNR, AIFitness, aif_fitted_r2, manual_aif_status, max_disp |
 | **T1** | T1_blood, T1_wm_median, T1_gm_median |
 | **Ktrans** | Ktrans_wm_median, Ktrans_gm_median, plus per-region medians (Hippo, PhG, Putamen, Pallidum, Thalamus, Caudate, Amygdala, Entorhinal cortex, Fusiform gyrus cortex/WM, Insula WM, Superior/Inferior temporal cortex, Posterior cingulate cortex, Medial temporal cortex) |
 | **Vp** | Per-region Vp medians (same regions as Ktrans) |
diff --git a/preprocess_all.sh b/preprocess_all.sh
index 9edf313..5fb0569 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -38,7 +38,6 @@ while getopts ":d:bBa:A:ZfhcC:j:mMsS:tl:T:w:p" options; do
 			AIF_SUFFIX=${OPTARG}
 			;;
 		A)
-			AUTO_AIF_PATH=$(find $HOME -wholename '*main_vif.py' -printf '%h\n' -quit || find / -name '*main_vif.py' -printf '%h\n' -quit) &> /dev/null
 			case "${OPTARG}" in
 				M)
 					USE_AUTO_AIF=0

From cc89ab8565f48613e61fc2c81cf2aad33eef43fe Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Wed, 26 Aug 2026 13:26:56 -0700
Subject: [PATCH 23/29] correct path search strings

---
 DCE_all.sh        | 4 ++--
 preprocess_all.sh | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/DCE_all.sh b/DCE_all.sh
index 2e73045..1151c9a 100755
--- a/DCE_all.sh
+++ b/DCE_all.sh
@@ -100,7 +100,7 @@ if [ -z "$DATA_DIR" ]
 fi
 if [[ "$OSTYPE" == "linux-gnu" ]]; then
 	# respect a pre-set path (e.g. from CI) instead of searching the whole filesystem
-	ROCKETSHIP_PATH=${ROCKETSHIP_PATH:-$(find $HOME -name '*run_dce_cli.m' -printf '%h\n' -quit || find / -name '*run_dce_cli.m' -printf '%h\n' -quit) 2> /dev/null}
+	ROCKETSHIP_PATH=${ROCKETSHIP_PATH:-$(find $HOME -name '*run_dce_cli.m' -printf '%h\n' -quit || find / -name '*run_dce_cli.m' -printf '%h\n' -quit 2> /dev/null)}
 	SCRIPT_PATH=$(dirname "$(realpath $0)")
 	GPUFIT_PATH=${GPUFIT_PATH:-$(find $HOME -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit || find / -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit)}
 	GPUFIT_M_PATH=${GPUFIT_M_PATH:-$(find $HOME -name 'ModelID.m' -printf '%h\n' -quit || find / -name 'ModelID.m' -printf '%h\n' -quit)}
@@ -259,7 +259,7 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	rm -f dce/dce_patlak_fit_rois.xls
 	if [ $USE_PYTHON -eq 1 ]
 		then
-		${ROCKETSHIP_PATH}/.venv/bin/python ${ROCKETSHIP_PATH}/run_dce_cli_python_case.py --subject-source $SUBJECT_TP_PATH --subject-tp $SUBJECT_TP_PATH --output-dir $SUBJECT_TP_PATH --events off
+		${ROCKETSHIP_PATH}/.venv/bin/python ${ROCKETSHIP_PATH}/run_dce_python_case.py --subject-source $SUBJECT_TP_PATH --subject-tp $SUBJECT_TP_PATH --output-dir $SUBJECT_TP_PATH --events off
 	else
 		matlab -nodisplay -r "cd('$ROCKETSHIP_PATH'); addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; run_dce_cli('$DATA_DIR/$SUBJECT/$SESSION/', '$SUBJECT_TP_PATH/'); exit;"
 	fi
diff --git a/preprocess_all.sh b/preprocess_all.sh
index 5fb0569..9089ba9 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -76,7 +76,6 @@ while getopts ":d:bBa:A:ZfhcC:j:mMsS:tl:T:w:p" options; do
 			DATE=$(date +%Y-%m-%d)
 			# derivatives dir is up 2 levels from data dir
 			DERIV_DIR=$(dirname $(dirname $DATA_DIR))/derivatives
-			echo $DERIV_DIR
 			if [ ! -d "$DERIV_DIR" ]
 				then
 				mkdir -p "$DERIV_DIR"

From 3209acedaf181ee356c0a1befed1ee33bbf58d52 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Thu, 27 Aug 2026 12:57:55 -0700
Subject: [PATCH 24/29] fix actions path to autoAIF weights

---
 .github/workflows/DCE.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 5571bab..a68f1f2 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -39,7 +39,7 @@ jobs:
         pip install --upgrade hd-bet
 
     - name: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -A A
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -A A -w /home/mrispec/Code/DCEPrep/docker/files/model_weight_huber1.h5
       
     - name: Run DCE
       run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f
@@ -100,7 +100,7 @@ jobs:
         pip install --upgrade hd-bet
 
     - name: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p -A A
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p -A A -w /home/mrispec/Code/DCEPrep/docker/files/model_weight_huber1.h5
       
     - name: Run DCE
       run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f -p

From ca307f15c9faeed37c9f117f0455639dcfdbea20 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Thu, 27 Aug 2026 13:23:05 -0700
Subject: [PATCH 25/29] hopeful autoAIF weight path fix for runner

---
 preprocess_all.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/preprocess_all.sh b/preprocess_all.sh
index 9089ba9..644db1c 100755
--- a/preprocess_all.sh
+++ b/preprocess_all.sh
@@ -758,7 +758,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 		if [ $EN_MOTION_CORR -eq 1 ]
 			then
 			"$AUTO_AIF_PYTHON" $AUTO_AIF_PATH/main_vif.py --mode inference --input_path dce/${PREFIX}_desc-hmc_DCE.nii.gz --save_output_path $PWD/dce \
-				--model_weight_path $SCRIPT_PATH/$AUTOAIF_WEIGHT_PATH \
+				--model_weight_path $AUTOAIF_WEIGHT_PATH \
 				--model_name $AUTOAIF_MODEL \
 				--save_image 1 &> dce/${PREFIX}_desc-autoaif.log
 			if [ ! -f "dce/${PREFIX}_desc-hmc_DCE_float_mask.nii" ] || [ ! -f "dce/${PREFIX}_desc-hmc_DCE_mask.nii" ]; then
@@ -776,7 +776,7 @@ for source_dir in $DATA_DIR/$SCRIPT_LOOP_DIRS; do
 			fslmaths anat/${PREFIX}_${REF_SPACE}_T1map.nii.gz -mas dce/${PREFIX}_label-AIF_desc-topvoxels_mask.nii dce/${PREFIX}_label-AIF_T1map.nii
 		else
 			"$AUTO_AIF_PYTHON" $AUTO_AIF_PATH/main_vif.py --mode inference --input_path $source_dir/dce/${PREFIX}_DCE.nii.gz --save_output_path $PWD/dce \
-				--model_weight_path $SCRIPT_PATH/$AUTOAIF_WEIGHT_PATH \
+				--model_weight_path $AUTOAIF_WEIGHT_PATH \
 				--model_name $AUTOAIF_MODEL \
 				--save_image 1 &> dce/${PREFIX}_desc-autoaif.log
 			if [ ! -f "dce/${PREFIX}_DCE_float_mask.nii" ] || [ ! -f "dce/${PREFIX}_DCE_mask.nii" ]; then

From 7979f10ec251b2d16862d698e1503721f6e408cc Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Thu, 27 Aug 2026 14:00:45 -0700
Subject: [PATCH 26/29] remove PDF gen/upload from actions

---
 .github/workflows/DCE.yml | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index a68f1f2..5942b65 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -50,9 +50,9 @@ jobs:
         cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/preprocessing_log_${date}.txt
         cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/dce_log_${date}.txt
 
-    - name: Convert HTML to PDF
-      run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
-      continue-on-error: true
+    # - name: Convert HTML to PDF
+    #   run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+    #   continue-on-error: true
 
     - name: Validate analysis results
       run: |
@@ -66,7 +66,6 @@ jobs:
         name: HTML_report
         path: |
           /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
-          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
           /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/
         retention-days: 7
         if-no-files-found: error
@@ -111,9 +110,9 @@ jobs:
         cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/preprocessing_log_${date}.txt
         cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/dce_log_${date}.txt
 
-    - name: Convert HTML to PDF
-      run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
-      continue-on-error: true
+    # - name: Convert HTML to PDF
+    #   run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+    #   continue-on-error: true
 
     - name: Validate analysis results
       run: |
@@ -127,7 +126,6 @@ jobs:
         name: HTML_report
         path: |
           /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
-          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
           /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/
         retention-days: 7
         if-no-files-found: error

From 0c01fdffd47687b3ba6aea1d4ad3e5c80ba66758 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Thu, 27 Aug 2026 14:12:40 -0700
Subject: [PATCH 27/29] missed a spot

---
 .github/workflows/DCE.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/DCE.yml b/.github/workflows/DCE.yml
index 5942b65..2f902c1 100644
--- a/.github/workflows/DCE.yml
+++ b/.github/workflows/DCE.yml
@@ -57,7 +57,6 @@ jobs:
     - name: Validate analysis results
       run: |
         test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
-        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
         test -n "$(find /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/ -type f -print -quit)"
 
     - name: Upload analysis results
@@ -117,7 +116,6 @@ jobs:
     - name: Validate analysis results
       run: |
         test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
-        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
         test -n "$(find /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/ -type f -print -quit)"
 
     - name: Upload analysis results

From 73a01b7445e8ef2b6f357d81edbc1d05fdc58d61 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Fri, 28 Aug 2026 18:58:10 -0700
Subject: [PATCH 28/29] Refactor path resolution for ROCKETSHIP and GPUFIT,
 enhance error handling, and update output file naming conventions to include
 gzip compression.

---
 DCE_all.sh | 56 ++++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 44 insertions(+), 12 deletions(-)

diff --git a/DCE_all.sh b/DCE_all.sh
index 1151c9a..f797fde 100755
--- a/DCE_all.sh
+++ b/DCE_all.sh
@@ -98,12 +98,43 @@ if [ -z "$DATA_DIR" ]
 		echo "ERROR: Please use '-d [dir_path]' to pass the path to your main data directory to this script."
 		exit 1
 fi
+
+resolve_tool_path() {
+	local configured_path=$1
+	local marker_file=$2
+	shift 2
+	local candidate_path
+
+	if [ -n "$configured_path" ]; then
+		if [ -f "$configured_path/$marker_file" ]; then
+			printf '%s\n' "$configured_path"
+			return 0
+		fi
+		echo "ERROR: Configured path $configured_path does not contain $marker_file." >&2
+		return 1
+	fi
+
+	for candidate_path in "$@"; do
+		if [ -f "$candidate_path/$marker_file" ]; then
+			printf '%s\n' "$candidate_path"
+			return 0
+		fi
+	done
+
+	find "$HOME" \
+		\( -path "$HOME/.local/share/Trash" -o -path "$HOME/.local/share/Trash/*" -o -path "$HOME/.Trash" -o -path "$HOME/.Trash/*" \) -prune -o \
+		-type f -name "$marker_file" -printf '%h\n' -quit 2> /dev/null
+}
+
 if [[ "$OSTYPE" == "linux-gnu" ]]; then
-	# respect a pre-set path (e.g. from CI) instead of searching the whole filesystem
-	ROCKETSHIP_PATH=${ROCKETSHIP_PATH:-$(find $HOME -name '*run_dce_cli.m' -printf '%h\n' -quit || find / -name '*run_dce_cli.m' -printf '%h\n' -quit 2> /dev/null)}
+	ROCKETSHIP_PATH=$(resolve_tool_path "${ROCKETSHIP_PATH:-}" "run_dce_cli.m" "/opt/ROCKETSHIP/ROCKETSHIP-dev")
 	SCRIPT_PATH=$(dirname "$(realpath $0)")
-	GPUFIT_PATH=${GPUFIT_PATH:-$(find $HOME -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit || find / -name 'GpufitConstrainedMex.mexa64' -printf '%h\n' -quit)}
-	GPUFIT_M_PATH=${GPUFIT_M_PATH:-$(find $HOME -name 'ModelID.m' -printf '%h\n' -quit || find / -name 'ModelID.m' -printf '%h\n' -quit)}
+	GPUFIT_PATH=$(resolve_tool_path "${GPUFIT_PATH:-}" "GpufitConstrainedMex.mexa64" "/opt/Gpufit/matlab64")
+	GPUFIT_M_PATH=$(resolve_tool_path "${GPUFIT_M_PATH:-}" "ModelID.m" "/opt/Gpufit/matlab")
+	if [ -z "$ROCKETSHIP_PATH" ] || [ -z "$GPUFIT_PATH" ] || [ -z "$GPUFIT_M_PATH" ]; then
+		echo "ERROR: Unable to locate ROCKETSHIP or GPUfit. Set ROCKETSHIP_PATH, GPUFIT_PATH, and GPUFIT_M_PATH to directories containing their required MATLAB files." >&2
+		exit 1
+	fi
 else
 	ROCKETSHIP_PATH=$(find $HOME -type d -name ROCKETSHIP)
 	SCRIPT_PATH=$(find $HOME -type d -name in-house_toolbox)
@@ -259,17 +290,18 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	rm -f dce/dce_patlak_fit_rois.xls
 	if [ $USE_PYTHON -eq 1 ]
 		then
-		${ROCKETSHIP_PATH}/.venv/bin/python ${ROCKETSHIP_PATH}/run_dce_python_case.py --subject-source $SUBJECT_TP_PATH --subject-tp $SUBJECT_TP_PATH --output-dir $SUBJECT_TP_PATH --events off
+		${ROCKETSHIP_PATH}/.venv/bin/python ${ROCKETSHIP_PATH}/run_dce_python_case.py --subject-source "$DATA_DIR/$SUBJECT/$SESSION/" --subject-tp $SUBJECT_TP_PATH --output-dir $SUBJECT_TP_PATH --events off
 	else
 		matlab -nodisplay -r "cd('$ROCKETSHIP_PATH'); addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; run_dce_cli('$DATA_DIR/$SUBJECT/$SESSION/', '$SUBJECT_TP_PATH/'); exit;"
 	fi
-	mv dce/dce_*_fit_Ktrans.nii dce/${PREFIX}_Ktrans.nii
-	mv dce/dce_*_fit_ktrans_ci_low.nii dce/${PREFIX}_Ktrans_ci_low.nii
-	mv dce/dce_*_fit_ktrans_ci_high.nii dce/${PREFIX}_Ktrans_ci_high.nii
-	mv dce/dce_*_fit_vp.nii dce/${PREFIX}_vp.nii
-	mv dce/dce_*_fit_vp_ci_low.nii dce/${PREFIX}_vp_ci_low.nii
-	mv dce/dce_*_fit_vp_ci_high.nii dce/${PREFIX}_vp_ci_high.nii
-	mv dce/dce_*_fit_sse.nii dce/${PREFIX}_sse.nii
+	gzip dce/*.nii
+	mv dce/*_fit_*trans.nii.gz dce/${PREFIX}_Ktrans.nii.gz
+	mv dce/*_fit_*trans_ci_low.nii.gz dce/${PREFIX}_desc-cilow_Ktrans.nii.gz
+	mv dce/*_fit_*trans_ci_high.nii.gz dce/${PREFIX}_desc-cihigh_Ktrans.nii.gz
+	mv dce/*_fit_vp.nii.gz dce/${PREFIX}_vp.nii.gz
+	mv dce/*_fit_vp_ci_low.nii.gz dce/${PREFIX}_desc-cilow_vp.nii.gz
+	mv dce/*_fit_vp_ci_high.nii.gz dce/${PREFIX}_desc-cihigh_vp.nii.gz
+	mv dce/*_fit_sse.nii.gz dce/${PREFIX}_sse.nii.gz
 	# move images into figures folder
 	mv dce/dce*.png figures/
 	rm -f dce/*.fig

From 9c08ddb8625d31ff234f43bfee9bb85321fff8a4 Mon Sep 17 00:00:00 2001
From: Lucas Saca <LLSaca@llu.edu>
Date: Tue, 1 Sep 2026 13:54:09 -0700
Subject: [PATCH 29/29] gzip all DCE nii outputs, fix log output w/ w/o -p, fix
 plot_anat coord cuts, fix caserep aif NaNs, fix rawdata->sourcedata/raw refs,
 fix a couple other naming changes, fix exclude sheet key diffs

---
 DCE_all.sh           | 22 ++++++++++++++--------
 case_report.py       | 26 ++++++++++++++++----------
 ktrans_report.py     |  2 +-
 population_report.py | 12 ++++++------
 4 files changed, 37 insertions(+), 25 deletions(-)

diff --git a/DCE_all.sh b/DCE_all.sh
index f797fde..70d8ec8 100755
--- a/DCE_all.sh
+++ b/DCE_all.sh
@@ -294,7 +294,7 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	else
 		matlab -nodisplay -r "cd('$ROCKETSHIP_PATH'); addpath '$GPUFIT_PATH'; addpath '$GPUFIT_M_PATH'; run_dce_cli('$DATA_DIR/$SUBJECT/$SESSION/', '$SUBJECT_TP_PATH/'); exit;"
 	fi
-	gzip dce/*.nii
+	gzip dce/*.nii &> /dev/null
 	mv dce/*_fit_*trans.nii.gz dce/${PREFIX}_Ktrans.nii.gz
 	mv dce/*_fit_*trans_ci_low.nii.gz dce/${PREFIX}_desc-cilow_Ktrans.nii.gz
 	mv dce/*_fit_*trans_ci_high.nii.gz dce/${PREFIX}_desc-cihigh_Ktrans.nii.gz
@@ -303,12 +303,18 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	mv dce/*_fit_vp_ci_high.nii.gz dce/${PREFIX}_desc-cihigh_vp.nii.gz
 	mv dce/*_fit_sse.nii.gz dce/${PREFIX}_sse.nii.gz
 	# move images into figures folder
-	mv dce/dce*.png figures/
+	mv dce/dce*.png figures/ &> /dev/null
 	rm -f dce/*.fig
-	if [ ! -f "dce/${PREFIX}_Ktrans.nii" ]
+	if [ ! -f "dce/${PREFIX}_Ktrans.nii.gz" ]
 		then
 			echo $dir "Missing Ktrans maps. DCE failed or inputs were not generated. Hopefully message below is relevant." >> $LOG_FILE
-			tail -1 dce/A_dceR1info.log >> $LOG_FILE
+			if [ $USE_PYTHON -eq 1 ] && [ -f "reports/dce_pipeline_events.jsonl" ]
+				then
+				tail -1 reports/dce_pipeline_events.jsonl >> $LOG_FILE
+			elif [ -f "dce/A_dceR1info.log" ]
+				then
+				tail -1 dce/A_dceR1info.log >> $LOG_FILE
+			fi
 			cd $DATA_DIR/../derivatives
 			fail=1
 			continue
@@ -334,9 +340,9 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 	fslmaths anat/${PREFIX}_space-DCEref_T1map.nii -mas anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz anat/${PREFIX}_space-DCEref_label-CSF_T1map.nii
 
 	# Apply masks to Ktrans map
-	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-WM_mask.nii.gz dce/${PREFIX}_label-WM_Ktrans.nii
-	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-GM_mask.nii.gz dce/${PREFIX}_label-GM_Ktrans.nii
-	fslmaths dce/${PREFIX}_Ktrans.nii -mas anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz dce/${PREFIX}_label-CSF_Ktrans.nii
+	fslmaths dce/${PREFIX}_Ktrans.nii.gz -mas anat/${PREFIX}_space-DCEref_label-WM_mask.nii.gz dce/${PREFIX}_label-WM_Ktrans.nii.gz
+	fslmaths dce/${PREFIX}_Ktrans.nii.gz -mas anat/${PREFIX}_space-DCEref_label-GM_mask.nii.gz dce/${PREFIX}_label-GM_Ktrans.nii.gz
+	fslmaths dce/${PREFIX}_Ktrans.nii.gz -mas anat/${PREFIX}_space-DCEref_label-CSF_mask.nii.gz dce/${PREFIX}_label-CSF_Ktrans.nii.gz
 
 	# registration QC
 	python3 $SCRIPT_PATH/ktrans_analysis.py $dir $PREFIX
@@ -392,7 +398,7 @@ for der_dir in $SCRIPT_LOOP_DIR; do
 		# 	--metric MI[ $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz,anat/${PREFIX}_space-DCEref_T1w.nii.gz,1,32,Regular,0.25 ] \
 		# 	--convergence [ 1000x500x250x100,1e-6,10 ] --shrink-factors 12x8x4x2 --smoothing-sigmas 4x3x2x1vox
 		# antsApplyTransforms -i dce/${PREFIX}_Ktrans.nii -r $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -t ${PREFIX}_space-MNI_T1w0Warp.nii.gz -t t1w_MNI0GenericAffine.mat -t [T1_dyn0GenericAffine.mat, 1] -o Ktrans_MNI.nii.gz
-		antsApplyTransforms -i dce/${PREFIX}_Ktrans.nii -r $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -t anat/${PREFIX}_space-MNI_T1w0GenericAffine.mat -t [ anat/${PREFIX}_from-T1w_to-DCEref.mat, 1] -o dce/${PREFIX}_space-MNI_Ktrans.nii.gz
+		antsApplyTransforms -i dce/${PREFIX}_Ktrans.nii.gz -r $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -t anat/${PREFIX}_space-MNI_T1w0GenericAffine.mat -t [ anat/${PREFIX}_from-T1w_to-DCEref.mat, 1] -o dce/${PREFIX}_space-MNI_Ktrans.nii.gz
 		# antsApplyTransforms -i dce_patlak_fit_vp.nii -r $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -t t1w_MNI1Warp.nii.gz -t t1w_MNI0GenericAffine.mat -t [T1_dyn0GenericAffine.mat, 1] -o vp_MNI.nii.gz
 		# flirt -in dce_patlak_fit_Ktrans.nii -ref $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz -out ktrans_2_MNI.nii.gz -init DCE2MNI.mat -applyxfm
 	else
diff --git a/case_report.py b/case_report.py
index 6eb06d7..356f95e 100644
--- a/case_report.py
+++ b/case_report.py
@@ -25,7 +25,7 @@
 # if source_dir[-1] == '/':
 #     source_dir = source_dir[:-1]
 
-files_to_reorient = [f'anat/{prefix}_flip-01_space-DCEref_VFA.nii.gz', f'dce/{prefix}_Ktrans.nii',
+files_to_reorient = [f'anat/{prefix}_flip-01_space-DCEref_VFA.nii.gz', f'dce/{prefix}_Ktrans.nii.gz',
                      f'anat/{prefix}_space-DCEref_T1w.nii.gz', f'anat/{prefix}_space-DCEref_label-WM_mask.nii.gz',
                      f'anat/{prefix}_space-DCEref_T1map.nii', f'anat/{prefix}_space-DCEref_label-brain_mask.nii.gz',
                      f'anat/{prefix}_space-DCEref_label-GM_mask.nii.gz', f'anat/{prefix}_space-DCEref_seg-wmparc_dseg.nii.gz',
@@ -70,7 +70,7 @@ def space_ras_path(path):
         try:
             subprocess.run(command, check=True)
             if nifti_stem(file) == f'dce/{prefix}_Ktrans':
-                ktrans = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_Ktrans.nii')))
+                ktrans = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_Ktrans.nii.gz')))
                 ktrans_data = ktrans.get_fdata()
                 ktrans_flipped = np.flip(ktrans_data, axis=1)
                 ktrans_flipped = nib.Nifti1Image(ktrans_flipped, ktrans.affine, ktrans.header)
@@ -84,8 +84,10 @@ def space_ras_path(path):
                 ktrans_z_slices = min(dimensions)
                 midpt = int(ktrans_coords-5*ktrans_z_slices/2)
                 max_coord = int(ktrans_coords-5*ktrans_z_slices)
-                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=range(ktrans_coords, midpt, -5), axes=axes[0], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False, colorbar=True)
-                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=range(midpt, max_coord, -5), axes=axes[1], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False)
+                coords1 = list(range(ktrans_coords, midpt, -5))
+                coords2 = list(range(midpt, max_coord, -5))
+                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=coords1, axes=axes[0], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False, colorbar=True)
+                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=coords2, axes=axes[1], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False)
                 plt.savefig('figures/ktrans.svg', bbox_inches='tight', pad_inches = 0)
                 plt.close()
         except Exception as e:
@@ -103,17 +105,19 @@ def space_ras_path(path):
         try:
             subprocess.run(command, check=True)
             if nifti_stem(file) == f'dce/{prefix}_Ktrans':
-                ktrans = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_Ktrans.nii')))
+                ktrans = nib.load(resolve_nifti_path(space_ras_path(f'dce/{prefix}_Ktrans.nii.gz')))
                 ktrans_data = ktrans.get_fdata()
                 ktrans_flipped = np.flip(ktrans_data, axis=1)
                 ktrans_flipped = nib.Nifti1Image(ktrans_flipped, ktrans.affine, ktrans.header)
                 dimensions = ktrans.header.get_data_shape()
                 voxel_size = ktrans.header.get_zooms()
+                range1 = list(range(-56, -21, 5))
+                range2 = list(range(-21, 13, 5))
 
                 # plot Ktrans, different coords
                 fig, axes = plt.subplots(nrows=2, ncols=1, figsize=(15, 5), gridspec_kw={'hspace': -.1, 'wspace': -.1}, dpi=300)
-                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=range(-56, -21, 5), axes=axes[0], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False, colorbar=True)
-                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=range(-21, 13, 5), axes=axes[1], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False)
+                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=range1, axes=axes[0], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False, colorbar=True)
+                plotting.plot_anat(ktrans_flipped, display_mode='z', cut_coords=range2, axes=axes[1], vmin=0, vmax=expected_ktrans_vmax, cmap='gnuplot', annotate=False)
                 plt.savefig('figures/ktrans.svg', bbox_inches='tight', pad_inches = 0)
                 plt.close()
         except Exception as e:
@@ -322,15 +326,17 @@ def space_ras_path(path):
     img = nib.load(resolve_nifti_path(f'{source_dir}/dce/{prefix}_DCE.nii.gz'))
     img_data = img.get_fdata()
 # binarize AIF
-aif_data[aif_data > 0] = 1
-aif_data[aif_data < 0] = 0
+aif_data = np.where(np.isfinite(aif_data) & (aif_data > 0), 1.0, 0.0)
 # mask DCE where AIF is 1
 # but first ensure that DCE and AIF have same number of dimensions
 if len(aif_data.shape) < len(img_data.shape):
     aif_data = np.expand_dims(aif_data, axis=-1)
 aif_data_roi = img_data * aif_data
 # sum AIF data for each time point, z-slice independent
-aif_curve = np.sum(aif_data_roi, axis=(0, 1, 2)) / np.sum(aif_data[aif_data > 0])
+aif_voxel_count = np.count_nonzero(aif_data)
+if aif_voxel_count == 0:
+    raise ValueError(f'AIF mask is empty after removing NaNs for {prefix}')
+aif_curve = np.sum(aif_data_roi, axis=(0, 1, 2)) / aif_voxel_count
 # divide by AIF mean of timepoints before contrast agent arrival
 baseline = get_baseline_from_curve(aif_curve)
 aif_curve_ratio = aif_curve / baseline
diff --git a/ktrans_report.py b/ktrans_report.py
index 1c140cc..6aa6d80 100644
--- a/ktrans_report.py
+++ b/ktrans_report.py
@@ -32,7 +32,7 @@
 curves.append(png_np_array)
 curves.append(mpimg.imread('figures/dceAIF_fitting.png'))
 curves.append(mpimg.imread('figures/dce_timecurves.png'))
-ktrans = nib.load('dce/' + prefix + '_Ktrans.nii')
+ktrans = nib.load('dce/' + prefix + '_Ktrans.nii.gz')
 analysis = mpimg.imread('figures/' + prefix + '_desc-analysis.png')
 zeros = mpimg.imread('figures/' + prefix + '_desc-zeros.png')
 aif_curve = mpimg.imread('figures/dceAIF_fitting.png')
diff --git a/population_report.py b/population_report.py
index 6dcf18c..6f21d17 100644
--- a/population_report.py
+++ b/population_report.py
@@ -168,7 +168,7 @@ def get_case_stats(subject_id, timepoint):
             total_timepoints.append(subject_id + '/' + timepoint)
             # Check for missing data in rawdata folder
             prefix = f"{subject_id}_{timepoint}"
-            rawdata_dir = os.path.join(dir, "../rawdata", subject_id, timepoint)
+            rawdata_dir = os.path.join(dir, "../sourcedata/raw", subject_id, timepoint)
             missing_files = []
             # Check for anat/prefix_T1w.nii.gz
             t1w_path = os.path.join(rawdata_dir, f"anat/{prefix}_T1w.nii.gz")
@@ -195,7 +195,7 @@ def get_case_stats(subject_id, timepoint):
             # read AIF curve by applying aif.nii to dce.nii
             try:
                 dce = os.path.join(dceprep_dir, subject_id, timepoint, f"dce/{subject_id}_{timepoint}_desc-bfcz_DCE.nii.gz")
-                aif = os.path.join(dceprep_dir, subject_id, timepoint, f"dce/{subject_id}_{timepoint}_desc-AIF_T1map.nii.gz")
+                aif = os.path.join(dceprep_dir, subject_id, timepoint, f"dce/{subject_id}_{timepoint}_label-AIF_T1map.nii.gz")
                 if os.path.exists(dce) and os.path.exists(aif):
                     # load files
                     dce_img = nib.load(dce)
@@ -257,7 +257,7 @@ def get_case_stats(subject_id, timepoint):
             else:
                 manual_aif_status = "AUTO"
             # get fields we want from json
-            json_file = os.path.join(dir, "../rawdata", subject_id, timepoint, f"dce/{subject_id}_{timepoint}_DCE.json")
+            json_file = os.path.join(dir, "../sourcedata/raw", subject_id, timepoint, f"dce/{subject_id}_{timepoint}_DCE.json")
             try:
                 with open(json_file, 'r') as f:
                     data = json.load(f)
@@ -465,7 +465,7 @@ def get_case_stats(subject_id, timepoint):
                 return
             # read ktrans map
             try:
-                ktrans_map = os.path.join(dceprep_dir, subject_id, timepoint, f"dce/{subject_id}_{timepoint}_Ktrans.nii")
+                ktrans_map = os.path.join(dceprep_dir, subject_id, timepoint, f"dce/{subject_id}_{timepoint}_Ktrans.nii.gz")
                 ktrans_map = nib.load(ktrans_map)
                 ktrans_map = ktrans_map.get_fdata()
             except:
@@ -513,7 +513,7 @@ def get_case_stats(subject_id, timepoint):
             error = ""
             try:
                 prefix = f"{subject_id}_{timepoint}"
-                wmparc_path = os.path.join(dceprep_dir, subject_id, timepoint, f"anat/{prefix}_space-DCEref_desc-wmparc.nii.gz")
+                wmparc_path = os.path.join(dceprep_dir, subject_id, timepoint, f"anat/{prefix}_space-DCEref_seg-wmparc_dseg.nii.gz")
                 if os.path.isfile(wmparc_path):
                     wmparc = nib.load(wmparc_path)
                     wmparc = wmparc.get_fdata()
@@ -2573,7 +2573,7 @@ def get_case_stats(subject_id, timepoint):
 if len(population_data_exclude) > 0:
     df_exclude = pd.DataFrame(population_data_exclude)
     df_exclude = df_exclude.T
-    df_exclude = df_exclude[order_exclude]
+    df_exclude = df_exclude.reindex(columns=order_exclude)
     df_exclude.index.name = "Subject_ID"
     df_exclude.to_excel(writer, sheet_name='Pre-Exclude')
     for column in df_exclude.columns: