From 48f4c82141b1e5393720096a7fdb4b769c756ef3 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 14:33:52 -0400
Subject: [PATCH 01/18] Actions away!

---
 .github/workflows/collect_data.yml | 51 +++++++++++++++++++++++++
 .github/workflows/run_petprep.yml  | 60 ++++++++++++++++++++++++++++++
 2 files changed, 111 insertions(+)
 create mode 100644 .github/workflows/collect_data.yml
 create mode 100644 .github/workflows/run_petprep.yml

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
new file mode 100644
index 00000000..f0d70140
--- /dev/null
+++ b/.github/workflows/collect_data.yml
@@ -0,0 +1,51 @@
+Name: Collect Data
+
+On:
+  workflow_dispatch:
+  push:
+    branches: [ "main" ]
+    tags: "*"
+  pull_request:
+
+env:
+  DATA_DIR: /tmp/data/petprep_test_data
+  DERIVATIVES: "petprep freesurfer smriprep"
+
+Jobs:
+  collect-data:
+    outputs:
+      data_directory: ${{ env.DATA_DIR }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 200
+          fetch-tags: true
+      
+      - name: Check if data directory exists and has data
+        id: check-data
+        run: |
+          if [ -d "$DATA_DIR" ] && [ -n "$(ls -A $DATA_DIR 2>/dev/null)" ]; then
+            echo "Data directory exists and contains data, skipping collection"
+            echo "skip_collection=true" >> $GITHUB_OUTPUT
+          else
+            echo "Data directory is empty or does not exist, re-downloading data"
+            echo "skip_collection=false" >> $GITHUB_OUTPUT
+            # Clean up empty directory if it exists
+            if [ -d "$DATA_DIR" ]; then
+              echo "Removing empty data directory"
+              rm -rf "$DATA_DIR"
+            fi
+          fi
+      
+      - name: Collect data
+        if: steps.check-data.outputs.skip_collection != 'true'
+        run: |
+          uv run scripts/collect_test_data.py -o "$DATA_DIR" -d $DERIVATIVES
+      
+      - name: Data collection skipped
+        if: steps.check-data.outputs.skip_collection == 'true'
+        run: |
+          echo "Data collection step skipped - using existing data in $DATA_DIR"
+      
+     
\ No newline at end of file
diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
new file mode 100644
index 00000000..811a7c7a
--- /dev/null
+++ b/.github/workflows/run_petprep.yml
@@ -0,0 +1,60 @@
+name: Run PETPREP
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "main" ]
+    tags: "*"
+  pull_request:
+
+env:
+  DATA_DIR: /tmp/data/petprep_test_data
+
+jobs:
+  collect-data:
+    uses: ./.github/workflows/collect_data.yml
+
+  run-tests:
+    needs: collect-data
+    runs-on: baremetal
+    env:
+      DATA_DIR: ${{ needs.collect-data.outputs.data_directory }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 200
+          fetch-tags: true
+      
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Build and Install PETPREP
+        run: |
+          uv build 
+          pip install dist/*.whl
+
+      - name: Check petprep is installed
+        run: |
+          which petprep
+          petprep --version
+
+      - name: Verify test data exists
+        run: |
+          if [ ! -d "$DATA_DIR" ] || [ -z "$(ls -A $DATA_DIR 2>/dev/null)" ]; then
+            echo "Error: Test data directory is empty or missing"
+            exit 1
+          fi
+          echo "Test data verified at $DATA_DIR"
+          ls -la "$DATA_DIR"
+
+      - name: Run petprep
+        run: |
+          petprep "$DATA_DIR" "$DATA_DIR/derivatives/petprep" participant --fs-license-file "$FREESURFER_HOME/license.txt"
\ No newline at end of file

From 841b972f20b3e43d5dadc3b291b6366af498cdab Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 14:35:43 -0400
Subject: [PATCH 02/18] fix capital

---
 .github/workflows/collect_data.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index f0d70140..332f74bc 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -11,7 +11,7 @@ env:
   DATA_DIR: /tmp/data/petprep_test_data
   DERIVATIVES: "petprep freesurfer smriprep"
 
-Jobs:
+jobs:
   collect-data:
     outputs:
       data_directory: ${{ env.DATA_DIR }}

From 4384be4e6f1c332ecaa4c66a148504d7fc287925 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 14:50:55 -0400
Subject: [PATCH 03/18] fix syntax

---
 .github/workflows/collect_data.yml | 5 +++--
 .github/workflows/run_petprep.yml  | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index 332f74bc..7c4712e1 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -1,6 +1,6 @@
-Name: Collect Data
+name: Collect Data
 
-On:
+on:
   workflow_dispatch:
   push:
     branches: [ "main" ]
@@ -15,6 +15,7 @@ jobs:
   collect-data:
     outputs:
       data_directory: ${{ env.DATA_DIR }}
+    runs-on: baremetal
     steps:
       - name: Checkout repository
         uses: actions/checkout@v5
diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 811a7c7a..101d81a2 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -27,7 +27,7 @@ jobs:
           fetch-tags: true
       
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
       

From 07fa0d8fa879b844cdc189c05b576e7ef0c016cc Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 14:53:45 -0400
Subject: [PATCH 04/18] local not baremetal

---
 .github/workflows/collect_data.yml | 3 ++-
 .github/workflows/run_petprep.yml  | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index 7c4712e1..8ea3f2c6 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -6,6 +6,7 @@ on:
     branches: [ "main" ]
     tags: "*"
   pull_request:
+  workflow_call:
 
 env:
   DATA_DIR: /tmp/data/petprep_test_data
@@ -15,7 +16,7 @@ jobs:
   collect-data:
     outputs:
       data_directory: ${{ env.DATA_DIR }}
-    runs-on: baremetal
+    runs-on: local
     steps:
       - name: Checkout repository
         uses: actions/checkout@v5
diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 101d81a2..71d611d2 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -16,7 +16,7 @@ jobs:
 
   run-tests:
     needs: collect-data
-    runs-on: baremetal
+    runs-on: local
     env:
       DATA_DIR: ${{ needs.collect-data.outputs.data_directory }}
     steps:

From 0f7e9ffa72646de33083d33a2ffb1a2b96ed7b6b Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 14:55:08 -0400
Subject: [PATCH 05/18] install uv

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

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index 8ea3f2c6..b1282c32 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -39,6 +39,11 @@ jobs:
               rm -rf "$DATA_DIR"
             fi
           fi
+       
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
       
       - name: Collect data
         if: steps.check-data.outputs.skip_collection != 'true'

From 1f174508eaaab8ec5ef4ce973b7d81dff79fd3b2 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:02:49 -0400
Subject: [PATCH 06/18] update inputs and outputs for collect_data.yml

---
 .github/workflows/collect_data.yml | 39 ++++++++++++++++++------------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index b1282c32..0ced3ef2 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -2,15 +2,23 @@ name: Collect Data
 
 on:
   workflow_dispatch:
-  push:
-    branches: [ "main" ]
-    tags: "*"
-  pull_request:
   workflow_call:
-
+    inputs:
+      data_directory:
+        type: string
+        required: false
+        default: /tmp/data/petprep_test_data
+      derivatives:
+        type: string
+        required: false
+        default: "petprep freesurfer smriprep"
+      outputs:
+        data_directory:
+          description: 'Path to "cached" data collected with `collect_test_data.py`'
+          value: ${{ inputs.data_directory }}
 env:
-  DATA_DIR: /tmp/data/petprep_test_data
-  DERIVATIVES: "petprep freesurfer smriprep"
+  DATA_DIR: ${{ inputs.data_directory }}
+  DERIVATIVES: ${{ inputs.derivatives }}
 
 jobs:
   collect-data:
@@ -39,20 +47,21 @@ jobs:
               rm -rf "$DATA_DIR"
             fi
           fi
-       
+      
       - name: Install uv
         run: |
           curl -LsSf https://astral.sh/uv/install.sh | sh
           echo "$HOME/.cargo/bin" >> $GITHUB_PATH
       
-      - name: Collect data
+      - name: Setup Git for DataLad
         if: steps.check-data.outputs.skip_collection != 'true'
         run: |
-          uv run scripts/collect_test_data.py -o "$DATA_DIR" -d $DERIVATIVES
+          # Configure Git for DataLad
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "actions@github.com"
       
-      - name: Data collection skipped
-        if: steps.check-data.outputs.skip_collection == 'true'
+      - name: Collect data
+        if: steps.check-data.outputs.skip_collection != 'true'
         run: |
-          echo "Data collection step skipped - using existing data in $DATA_DIR"
-      
-     
\ No newline at end of file
+          # Collect the data
+          uv run scripts/collect_test_data.py -o "$DATA_DIR" -d $DERIVATIVES

From c8ef98ef3c771b93edb3cbc66934f49c29e1f3bd Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:05:17 -0400
Subject: [PATCH 07/18] type is required

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

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index 0ced3ef2..ad6a4ea6 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -14,6 +14,7 @@ on:
         default: "petprep freesurfer smriprep"
       outputs:
         data_directory:
+          type: string
           description: 'Path to "cached" data collected with `collect_test_data.py`'
           value: ${{ inputs.data_directory }}
 env:

From ab79e9bf7db47e9f883cf6cd2417419d725fcfb8 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:09:08 -0400
Subject: [PATCH 08/18] indentation error

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

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index ad6a4ea6..4af2fc79 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -12,11 +12,11 @@ on:
         type: string
         required: false
         default: "petprep freesurfer smriprep"
-      outputs:
-        data_directory:
-          type: string
-          description: 'Path to "cached" data collected with `collect_test_data.py`'
-          value: ${{ inputs.data_directory }}
+    outputs:
+      data_directory:
+        type: string
+        description: 'Path to "cached" data collected with `collect_test_data.py`'
+        value: ${{ inputs.data_directory }}
 env:
   DATA_DIR: ${{ inputs.data_directory }}
   DERIVATIVES: ${{ inputs.derivatives }}

From a174fd10c961de4ca4d7fc3dae2d38a859e31439 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:10:07 -0400
Subject: [PATCH 09/18] outputs don't have a type

---
 .github/workflows/collect_data.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/collect_data.yml b/.github/workflows/collect_data.yml
index 4af2fc79..b2169bd0 100644
--- a/.github/workflows/collect_data.yml
+++ b/.github/workflows/collect_data.yml
@@ -14,7 +14,6 @@ on:
         default: "petprep freesurfer smriprep"
     outputs:
       data_directory:
-        type: string
         description: 'Path to "cached" data collected with `collect_test_data.py`'
         value: ${{ inputs.data_directory }}
 env:

From 4a65b4216882c0704cd3700008f1fe092879ef82 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:15:12 -0400
Subject: [PATCH 10/18] add path to freesurfer home

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

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 71d611d2..d97030fb 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -9,6 +9,7 @@ on:
 
 env:
   DATA_DIR: /tmp/data/petprep_test_data
+  FREESURFER_HOME: /usr/local/freesurfer/7.4.1
 
 jobs:
   collect-data:

From 4a742baf6b4999bf39fc61ccba793ce53902ec2e Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:24:40 -0400
Subject: [PATCH 11/18] run setup freesurfer before petprep

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

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index d97030fb..ccaaf0e3 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -58,4 +58,5 @@ jobs:
 
       - name: Run petprep
         run: |
+          ./$FREESURFER_HOME/SetUpFreeSurfer.sh
           petprep "$DATA_DIR" "$DATA_DIR/derivatives/petprep" participant --fs-license-file "$FREESURFER_HOME/license.txt"
\ No newline at end of file

From 68e2def1ef008122ec9727a7b926840c3076fe2d Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:28:23 -0400
Subject: [PATCH 12/18] update workflow

---
 .github/workflows/run_petprep.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index ccaaf0e3..3757eda0 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -58,5 +58,5 @@ jobs:
 
       - name: Run petprep
         run: |
-          ./$FREESURFER_HOME/SetUpFreeSurfer.sh
+          $FREESURFER_HOME/SetUpFreeSurfer.sh
           petprep "$DATA_DIR" "$DATA_DIR/derivatives/petprep" participant --fs-license-file "$FREESURFER_HOME/license.txt"
\ No newline at end of file

From cb31867098b2e5ac922fa9a72805b870914c1a3b Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:33:32 -0400
Subject: [PATCH 13/18] yeah I thought you had to source

---
 .github/workflows/run_petprep.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 3757eda0..75d49e59 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -8,8 +8,11 @@ on:
   pull_request:
 
 env:
+  # for local/self hosted runners one can assume that the 
   DATA_DIR: /tmp/data/petprep_test_data
   FREESURFER_HOME: /usr/local/freesurfer/7.4.1
+  SUBJECTS_DIR: $FREESURFER_HOME/subjects
+
 
 jobs:
   collect-data:
@@ -58,5 +61,5 @@ jobs:
 
       - name: Run petprep
         run: |
-          $FREESURFER_HOME/SetUpFreeSurfer.sh
+          source $FREESURFER_HOME/SetUpFreeSurfer.sh
           petprep "$DATA_DIR" "$DATA_DIR/derivatives/petprep" participant --fs-license-file "$FREESURFER_HOME/license.txt"
\ No newline at end of file

From 72a5e361f20ec45f6ce51407978a440121186657 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:39:41 -0400
Subject: [PATCH 14/18] love it

---
 .github/workflows/run_petprep.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 75d49e59..7e655774 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -9,7 +9,6 @@ on:
 
 env:
   # for local/self hosted runners one can assume that the 
-  DATA_DIR: /tmp/data/petprep_test_data
   FREESURFER_HOME: /usr/local/freesurfer/7.4.1
   SUBJECTS_DIR: $FREESURFER_HOME/subjects
 
@@ -61,5 +60,5 @@ jobs:
 
       - name: Run petprep
         run: |
-          source $FREESURFER_HOME/SetUpFreeSurfer.sh
-          petprep "$DATA_DIR" "$DATA_DIR/derivatives/petprep" participant --fs-license-file "$FREESURFER_HOME/license.txt"
\ No newline at end of file
+          source "${FREESURFER_HOME}/SetUpFreeSurfer.sh"
+          petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt"
\ No newline at end of file

From ae447bf19f5082f3dec1e10642af2344bae6ac5f Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 2 Sep 2025 16:42:52 -0400
Subject: [PATCH 15/18] thumbs up

---
 .github/workflows/run_petprep.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 7e655774..f1f42f51 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -10,8 +10,6 @@ on:
 env:
   # for local/self hosted runners one can assume that the 
   FREESURFER_HOME: /usr/local/freesurfer/7.4.1
-  SUBJECTS_DIR: $FREESURFER_HOME/subjects
-
 
 jobs:
   collect-data:
@@ -61,4 +59,7 @@ jobs:
       - name: Run petprep
         run: |
           source "${FREESURFER_HOME}/SetUpFreeSurfer.sh"
+          echo "FREESURFER_HOME: ${FREESURFER_HOME}"
+          echo "SUBJECTS_DIR: ${SUBJECTS_DIR}"
+          echo "FS_LICENSE: ${FS_LICENSE}"
           petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt"
\ No newline at end of file

From 1630f2151d0526a2dd7d1aa238c0f86fb1a275a4 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 3 Sep 2025 11:50:56 -0400
Subject: [PATCH 16/18] installed deps, update paths in workflow

---
 .github/workflows/run_petprep.yml | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index f1f42f51..3649f8fa 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -10,6 +10,12 @@ on:
 env:
   # for local/self hosted runners one can assume that the 
   FREESURFER_HOME: /usr/local/freesurfer/7.4.1
+  FSLDIR: /opt/conda/envs/petprep
+  FSL_OUTPUT_TYPE: NIFTI_GZ
+  AFNI_PATH: /opt/afni-latest
+  FSL_PATH: /opt/conda/envs/petprep/share/fsl/bin
+  ANTS_PATH: /opt/ants-2.6.2/bin
+  WORKBENCH_PATH: /opt/workbench/exe_linux64
 
 jobs:
   collect-data:
@@ -40,7 +46,7 @@ jobs:
       - name: Build and Install PETPREP
         run: |
           uv build 
-          pip install dist/*.whl
+          pip install dist/*.whl --force-reinstall
 
       - name: Check petprep is installed
         run: |
@@ -59,7 +65,10 @@ jobs:
       - name: Run petprep
         run: |
           source "${FREESURFER_HOME}/SetUpFreeSurfer.sh"
-          echo "FREESURFER_HOME: ${FREESURFER_HOME}"
-          echo "SUBJECTS_DIR: ${SUBJECTS_DIR}"
-          echo "FS_LICENSE: ${FS_LICENSE}"
+          export PATH="${AFNI_PATH}:${PATH}"
+          export PATH="${FSL_PATH}:${PATH}"
+          export PATH="${ANTS_PATH}:${PATH}"
+          export PATH="${WORKBENCH_PATH}:${PATH}"
+          export FSLDIR="${FSLDIR}"
+          export FSL_OUTPUT_TYPE="${FSL_OUTPUT_TYPE}"
           petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt"
\ No newline at end of file

From 16763b38f47da4c59a1e4befba5c37c7a1e4268a Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 3 Sep 2025 21:02:19 -0400
Subject: [PATCH 17/18] Update run_petprep.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

👍 🇩🇰
---
 .github/workflows/run_petprep.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 3649f8fa..4fed0d48 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -71,4 +71,4 @@ jobs:
           export PATH="${WORKBENCH_PATH}:${PATH}"
           export FSLDIR="${FSLDIR}"
           export FSL_OUTPUT_TYPE="${FSL_OUTPUT_TYPE}"
-          petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt"
\ No newline at end of file
+          petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt" --sloppy --derivatives anat=${DATA_DIR}/derivatives/smriprep --fs-subjects-dir ${DATA_DIR}/derivatives/freesurfer 

From d5abd49b5041fca545d8980288ec2c1f763eb34e Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 4 Sep 2025 08:52:39 -0400
Subject: [PATCH 18/18] Update .github/workflows/run_petprep.yml

---
 .github/workflows/run_petprep.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run_petprep.yml b/.github/workflows/run_petprep.yml
index 4fed0d48..b79672a5 100644
--- a/.github/workflows/run_petprep.yml
+++ b/.github/workflows/run_petprep.yml
@@ -71,4 +71,7 @@ jobs:
           export PATH="${WORKBENCH_PATH}:${PATH}"
           export FSLDIR="${FSLDIR}"
           export FSL_OUTPUT_TYPE="${FSL_OUTPUT_TYPE}"
-          petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt" --sloppy --derivatives anat=${DATA_DIR}/derivatives/smriprep --fs-subjects-dir ${DATA_DIR}/derivatives/freesurfer 
+          petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant \
+            --fs-license-file "${FREESURFER_HOME}/license.txt" \
+            --fs-subjects-dir ${DATA_DIR}/derivatives/freesurfer --fs-no-resume \
+            --sloppy -vv --derivatives anat=${DATA_DIR}/derivatives/smriprep