From d40972d0fd50f9373ae7ff9ab8ea054041e56d9a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 22 May 2023 13:55:18 -0400
Subject: [PATCH 1/5] add ci workflow to test latest

---
 .github/workflows/test_latest.yml | 68 +++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 .github/workflows/test_latest.yml

diff --git a/.github/workflows/test_latest.yml b/.github/workflows/test_latest.yml
new file mode 100644
index 0000000..745c584
--- /dev/null
+++ b/.github/workflows/test_latest.yml
@@ -0,0 +1,68 @@
+---
+name: test latest image
+
+on:
+  push:
+    branches: ['*']
+  schedule:
+  - cron: 0 0 1 * *
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  test_latest_image:
+
+    strategy:
+      matrix:
+        dataset: ['1', '2']
+      fail-fast: false
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y tree
+
+    - name: pull docker image
+      run: docker pull bids/tracula:latest
+
+    - name: print help and version
+      run: |
+        docker run -t --rm --read-only \
+              bids/tracula:latest --help
+        docker run -t --rm --read-only \
+              bids/tracula:latest -v
+
+    - name: get data
+      run: |
+        wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
+        bash get_data_from_osf.sh ds114_test${{ matrix.dataset }}
+        bash get_data_from_osf.sh ds114_test${{ matrix.dataset }}_freesurfer
+
+    - name: prepare output dir
+      run: |
+        mkdir -p ${HOME}/outputs${{ matrix.dataset }}
+
+    - name: participant level
+      run: |
+        docker run -t --rm \
+        -v ${HOME}/data/ds114_test${{ matrix.dataset }}:/bids_dataset \
+        -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \
+        -v ${HOME}/data/ds114_test${{ matrix.dataset }}_freesurfer:/freesurfer \
+          bids/tracula:latest \
+            /bids_dataset /outputs participant \
+            --participant_label 01 \
+            --license_key="~/test.key" \
+            --freesurfer_dir /freesurfer \
+            --stages prep
+
+        cat ${HOME}/outputs${{ matrix.dataset }}/sub-01/scripts/trac-preproc.done
+
+    - name: check output
+      run: tree ${HOME}/outputs${{ matrix.dataset }}

From a9b3e568a05a1e87f93d33703c1a8ef98c121023 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 22 May 2023 13:57:49 -0400
Subject: [PATCH 2/5] use the proper file

---
 .github/workflows/test_latest.yml | 175 ++++++++++++++++++------------
 1 file changed, 108 insertions(+), 67 deletions(-)

diff --git a/.github/workflows/test_latest.yml b/.github/workflows/test_latest.yml
index 745c584..72c4f02 100644
--- a/.github/workflows/test_latest.yml
+++ b/.github/workflows/test_latest.yml
@@ -1,68 +1,109 @@
 ---
-name: test latest image
-
-on:
-  push:
-    branches: ['*']
-  schedule:
-  - cron: 0 0 1 * *
-  workflow_dispatch:
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-jobs:
-
-  test_latest_image:
-
-    strategy:
-      matrix:
-        dataset: ['1', '2']
-      fail-fast: false
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Install dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y tree
-
-    - name: pull docker image
-      run: docker pull bids/tracula:latest
-
-    - name: print help and version
-      run: |
-        docker run -t --rm --read-only \
-              bids/tracula:latest --help
-        docker run -t --rm --read-only \
-              bids/tracula:latest -v
-
-    - name: get data
-      run: |
-        wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
-        bash get_data_from_osf.sh ds114_test${{ matrix.dataset }}
-        bash get_data_from_osf.sh ds114_test${{ matrix.dataset }}_freesurfer
-
-    - name: prepare output dir
-      run: |
-        mkdir -p ${HOME}/outputs${{ matrix.dataset }}
-
-    - name: participant level
-      run: |
-        docker run -t --rm \
-        -v ${HOME}/data/ds114_test${{ matrix.dataset }}:/bids_dataset \
-        -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \
-        -v ${HOME}/data/ds114_test${{ matrix.dataset }}_freesurfer:/freesurfer \
-          bids/tracula:latest \
-            /bids_dataset /outputs participant \
-            --participant_label 01 \
-            --license_key="~/test.key" \
-            --freesurfer_dir /freesurfer \
-            --stages prep
-
-        cat ${HOME}/outputs${{ matrix.dataset }}/sub-01/scripts/trac-preproc.done
-
-    - name: check output
-      run: tree ${HOME}/outputs${{ matrix.dataset }}
+  name: test latest image
+  
+  on:
+    push:
+      branches: ['*']
+    schedule:
+    - cron: 0 0 1 * *
+    workflow_dispatch:
+  
+  concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+  
+  jobs:
+  
+    test_version:
+  
+      runs-on: ubuntu-latest
+  
+      steps:
+  
+      - name: pull docker image
+        run: docker pull bids/mrtrix3_connectome:latest
+  
+      - name: print help and version
+        run: |
+          docker run -t --rm --read-only \
+            -v /tmp:/tmp \
+            -v /var/tmp:/var/tmp \
+                bids/tracula:latest --help
+          docker run -t --rm --read-only \
+            -v /tmp:/tmp \
+            -v /var/tmp:/var/tmp \
+                bids/mrtrix3_connectome:latest --version
+  
+    test_participant:
+  
+      runs-on: ubuntu-latest
+  
+      steps:
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y tree
+  
+      - name: pull docker image
+        run: docker pull bids/mrtrix3_connectome:latest
+  
+      - name: get data
+        run: |
+          mkdir -p ${HOME}/downloads
+          wget -c -O ${HOME}/downloads/preproc.tar.gz "https://osf.io/d9gx7/download"
+          mkdir -p ${HOME}/data
+          tar xf ${HOME}/downloads/preproc.tar.gz -C ${HOME}/data
+  
+      - name: prepare output dir
+        run: |
+          mkdir -p ${HOME}/outputs
+  
+      - name: Run preproc-level analysis for all subjects
+        run: |
+          docker run -t --rm --read-only \
+            -v /tmp:/tmp -v /var/tmp:/var/tmp \
+            -v ${HOME}/data/BIDS:/bids_dataset \
+            -v ${HOME}/data/outputs:/outputs \
+            -v ${HOME}/scratch:/scratch \
+              bids/mrtrix3_connectome \
+                /bids_dataset /outputs preproc --scratch /scratch
+  
+      - name: check output
+        run: tree ${HOME}/outputs
+          
+    test_group:
+  
+      runs-on: ubuntu-latest
+  
+      steps:
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y tree
+  
+      - name: pull docker image
+        run: docker pull bids/mrtrix3_connectome:latest
+  
+      - name: get data
+        run: |
+          mkdir -p ${HOME}/downloads
+          wget -c -O ${HOME}/downloads/group.tar.gz "https://osf.io/6s8bx/download"
+          mkdir -p ${HOME}/data
+          tar xf ${HOME}/downloads/group.tar.gz -C ${HOME}/data
+  
+      - name: prepare output dir
+        run: |
+          mkdir -p ${HOME}/outputs
+  
+      - name: Run preproc-level analysis for all subjects
+        run: |
+          docker run -t --rm --read-only \
+            -v /tmp:/tmp -v /var/tmp:/var/tmp \
+            -v ${HOME}/data/BIDS:/bids_dataset \
+            -v ${HOME}/data/outputs:/outputs \
+            -v ${HOME}/scratch:/scratch \
+              bids/mrtrix3_connectome \
+                /bids_dataset /outputs group --scratch /scratch
+  
+      - name: check output
+        run: tree ${HOME}/outputs
\ No newline at end of file

From a0464d0624e75a3d472655399275508eb22e7e68 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 22 May 2023 14:16:39 -0400
Subject: [PATCH 3/5] add participant level

---
 .github/workflows/test_latest.yml | 48 +++++++++++++++++++++++++++++--
 1 file changed, 45 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_latest.yml b/.github/workflows/test_latest.yml
index 72c4f02..ca5c438 100644
--- a/.github/workflows/test_latest.yml
+++ b/.github/workflows/test_latest.yml
@@ -34,7 +34,7 @@
             -v /var/tmp:/var/tmp \
                 bids/mrtrix3_connectome:latest --version
   
-    test_participant:
+    test_preproc:
   
       runs-on: ubuntu-latest
   
@@ -70,7 +70,49 @@
   
       - name: check output
         run: tree ${HOME}/outputs
-          
+
+    test_participant:
+  
+      runs-on: ubuntu-latest
+
+      steps:
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y tree
+
+      - name: pull docker image
+        run: docker pull bids/mrtrix3_connectome:latest
+
+      - name: get data
+        run: |
+          mkdir -p ${HOME}/downloads
+          wget -c -O ${HOME}/downloads/participant.tar.gz "https://osf.io/skc5x/download"
+          mkdir -p ${HOME}/data
+          tar xf ${HOME}/downloads/participant.tar.gz -C ${HOME}/data
+
+      - name: prepare output dir
+        run: |
+          mkdir -p ${HOME}/outputs
+
+      - name: Run preproc-level analysis for all subjects
+        run: |
+          docker run -t --rm --read-only \
+            -v /tmp:/tmp -v /var/tmp:/var/tmp \
+            -v ${HOME}/data/BIDS:/bids_dataset \
+            -v ${HOME}/data/outputs:/outputs \
+            -v ${HOME}/scratch:/scratch \
+              bids/mrtrix3_connectome \
+                /bids_dataset /outputs participant \
+                --scratch /scratch \
+                --parcellation aal \
+                --streamlines 100000 \
+                --output_verbosity 3
+
+
+      - name: check output
+        run: tree ${HOME}/outputs
+
     test_group:
   
       runs-on: ubuntu-latest
@@ -95,7 +137,7 @@
         run: |
           mkdir -p ${HOME}/outputs
   
-      - name: Run preproc-level analysis for all subjects
+      - name: Run group-level analysis
         run: |
           docker run -t --rm --read-only \
             -v /tmp:/tmp -v /var/tmp:/var/tmp \

From 7dfd1bfc341699d94d6dda0debd9fd4ad1b640bb Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 22 May 2023 14:27:04 -0400
Subject: [PATCH 4/5] pull the proper image

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

diff --git a/.github/workflows/test_latest.yml b/.github/workflows/test_latest.yml
index ca5c438..9634007 100644
--- a/.github/workflows/test_latest.yml
+++ b/.github/workflows/test_latest.yml
@@ -28,7 +28,7 @@
           docker run -t --rm --read-only \
             -v /tmp:/tmp \
             -v /var/tmp:/var/tmp \
-                bids/tracula:latest --help
+                bids/mrtrix3_connectome:latest --help
           docker run -t --rm --read-only \
             -v /tmp:/tmp \
             -v /var/tmp:/var/tmp \

From ae3ea40ff06bc4ec7174c6322832fc10d9dc6bd8 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 22 May 2023 14:34:32 -0400
Subject: [PATCH 5/5] do not ask for help

---
 .github/workflows/test_latest.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/test_latest.yml b/.github/workflows/test_latest.yml
index 9634007..31ddc50 100644
--- a/.github/workflows/test_latest.yml
+++ b/.github/workflows/test_latest.yml
@@ -25,10 +25,6 @@
   
       - name: print help and version
         run: |
-          docker run -t --rm --read-only \
-            -v /tmp:/tmp \
-            -v /var/tmp:/var/tmp \
-                bids/mrtrix3_connectome:latest --help
           docker run -t --rm --read-only \
             -v /tmp:/tmp \
             -v /var/tmp:/var/tmp \