[ENH] set up tests on NARPS dataset

.github/workflows/run_tests_narps.yml

@@ -0,0 +1,118 @@
+name: "matlab: narps dataset"
+
+on:
+
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches: ["*"]
+
+  # to trigger update manually from the Action tab in github
+  workflow_dispatch:
+    inputs:
+      log:
+        description: "run tests manually"
+        required: false
+
+jobs:
+
+  cache_test_data:
+
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: "Make cachedir"
+        run: |
+          mkdir -p /tmp/.cache/data && \
+          chmod 777 /tmp/.cache/data
+
+      - name: Set git ID
+        run: |
+          git config --global user.name 'bipdsm GH-Action User' && \
+          git config --global user.email 'remi_gau@hotmail.com'
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y git-annex
+          python -m pip install --upgrade pip
+          pip install datalad
+
+      - name: Datalad WTF
+        run: |
+         datalad wtf
+
+      - name: Install cached data
+        uses: actions/cache@v3
+        id: cache
+        with:
+          path: /tmp/.cache/data
+          key: ds001734-${{ github.ref_name }}-${{ github.sha }}
+          restore-keys: |
+            ds001734-${{ github.ref_name }}-
+            ds001734-
+
+      - name: "Install raw and fMRIPrep derivatives of ds001734"
+        run: |
+          cd /tmp/.cache/data
+          datalad install ///openneuro/ds001734
+          datalad install ///openneuro-derivatives/ds001734-fmriprep
+          cd  ds001734-fmriprep && \
+              datalad get sub-00[1-4]/anat/*MNI152NLin2009cAsym*mask.nii.gz \
+                          sub-00[1-4]/anat/*MNI152NLin2009cAsym*T1w.nii.gz \
+                          sub-00[1-4]/func/*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz \
+                          sub-*/func/*tsv	\
+                          sub-*/func/*json
+          datalad status
+
+  tests_matlab:
+
+    needs: [cache_test_data]
+
+    runs-on: ubuntu-22.04
+
+    steps:
+
+      - name: Clone bidspm
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Install MATLAB
+        uses: matlab-actions/setup-matlab@v1.2.3
+        with:
+          # MATLAB release to set up R2020a
+          release: R2020a
+
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+
+      - name: Install validators
+        run: make install
+
+      - name: Install SPM
+        run: |
+          git clone https://github.com/spm/spm12.git --depth 1
+
+      - name: Copy Macs toolbox to SPM inputs_folder
+        run: cp -rv lib/MACS spm12/toolbox/MACS
+
+      - name: Run commands
+        uses: matlab-actions/run-command@v1.1.2
+        with:
+          command: |
+            root_dir = getenv('GITHUB_WORKSPACE');
+            fprintf('\nroot dir is %s\n', root_dir);
+            addpath(fullfile(root_dir, 'spm12'));
+            cd(fullfile(root_dir, 'demos', 'openneuro'));
+            run ds001734_run;

.github/workflows/test_narps.m

@@ -0,0 +1,50 @@
+%
+% Analysis of the NARPS dataset
+%
+% (C) Copyright 2022 bidspm developers
+
+clear;
+clc;
+
+root_dir = getenv('GITHUB_WORKSPACE');
+
+addpath(fullfile(pwd, '..', '..'));
+bidspm();
+
+% The directory where the data are located
+bids_dir = '/tmp/.cache/data/ds001734';
+fmriprep_dir =  '/tmp/.cache/data/ds001734-fmriprep';
+output_dir = fullfile(root_dir, 'outputs', 'ds001734', 'derivatives');
+
+subject_label = {'001', '002', '003', '004'};
+task = {'MGT'};
+space = {'MNI152NLin2009cAsym'};
+
+bidspm(fmriprep_dir, output_dir, 'subject', ...
+       'action', 'smooth', ...
+       'participant_label', subject_label, ...
+       'task', task, ...
+       'space', space, ...
+       'fwhm', 8);
+
+%% Statistics
+
+preproc_dir = fullfile(root_dir, 'outputs', 'ds001734', 'derivatives', 'bidspm-preproc');
+model_file = fullfile(returnRootDir, ...
+                      'demos', ...
+                      'openneuro', ...
+                      'models', ...
+                      'model-narps_desc-U26C_smdl.json');
+
+%% Subject level analysis
+
+bidspm(bids_dir, output_dir, 'subject', ...
+       'action', 'stats', ...
+       'participant_label', subject_label, ...
+       'preproc_dir', preproc_dir, ...
+       'model_file', model_file, ...
+       'ignore', {'slice_timing'}, ...
+       'skip_validation', true, ...
+       'verbosity', 0, ...
+       'space', space, ...
+       'fwhm', 8);

.gitignore

@@ -1,5 +1,3 @@
-
-
 # General
 .DS_Store
 
@@ -9,6 +7,7 @@
 *.html
 *.ps
 
+new_events.tsv
 
 tmp
 

demos/openneuro/Makefile

@@ -29,6 +29,17 @@ data_ds001168:
 	cd inputs && datalad install ///openneuro/ds001168
 	cd inputs/ds001168 && datalad get ds001168/sub-0[12]
 
+data_ds001734:
+	mkdir -p inputs
+	cd inputs && datalad install ///openneuro/ds001734
+	cd inputs && datalad install ///openneuro-derivatives/ds001734-fmriprep
+	cd inputs/ds001734-fmriprep && datalad get sub-00[1]/anat/*MNI152NLin2009cAsym*mask.nii.gz
+	cd inputs/ds001734-fmriprep && datalad get sub-00[1]/anat/*MNI152NLin2009cAsym*T1w.nii.gz
+	cd inputs/ds001734-fmriprep && datalad get sub-00[1]/func/*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz
+	cd inputs/ds001734-fmriprep && datalad get sub-*/func/*tsv
+	cd inputs/ds001734-fmriprep && datalad get sub-*/func/*json
+
+
 data_ds002799:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds002799

demos/openneuro/README.md

@@ -1,8 +1,8 @@
 # Demos based on openneuro datasets
 
 -   ds000001: one task, one session, several runs
--   ds000114: several tasks, several sessions,
-    one or several runs depending on task
+-   ds000114: several tasks, several sessions, one or several runs depending on
+    task
 -   ds001168: resting state, several sessions, several acquisition, fieldmaps,
     physio data
 -   ds002799: resting state and task, several sessions, with fmriprep data
@@ -15,8 +15,8 @@ All those data can be installed with
 Datalad datasets can be accessed via their siblings on:
 https://github.com/OpenNeuroDatasets
 
-Check the content of the `Makefile` to see the code snippets you need to run
-to install those datasets.
+Check the content of the `Makefile` to see the code snippets you need to run to
+install those datasets.
 
 Otherwise you can also get them by using the Datalad superdataset.
 
@@ -31,3 +31,41 @@ cd openneuro/dsXXXXXX
 # get rest data first subject
 datalad get /openneuro/dsXXXXXX/sub-0001/func/sub-0001*
 ```
+
+## NARPS: ds001734
+
+More details here:
+
+https://docs.google.com/spreadsheets/d/1FU_F6kdxOD4PRQDIHXGHS4zTi_jEVaUqY_Zwg0z6S64/edit#gid=1019165812&range=A51
+
+TODO: add expected value to the model
+
+```matlab
+% compute euclidean distance to the indifference line defined by
+% gain twice as big as losses
+% https://en.wikipedia.org/wiki/Distance_from_a_point_to_a_line
+a = 0.5;
+b = -1;
+c = 0;
+x = onsets{iRun}.gain;
+y = onsets{iRun}.loss;
+dist = abs(a * x + b * y + c) / (a^2 + b^2)^.5;
+onsets{iRun}.EV = dist; % create an "expected value" regressor
+```
+
+TODO: transformers cannot yet be appled to confounds
+
+```json
+{
+    "Description": "Time points with a framewise displacement (as calculated by fMRIprep) > 0.5 mm were censored (no interpolation) at the subject level GLM..",
+    "Name": "Threshold",
+    "Input": [
+        "framewise_displacement"
+    ],
+    "Threshold": 0.5,
+    "Binarize": true,
+    "Output": [
+        "thres_framewise_displacement"
+    ]
+},
+```

demos/openneuro/ds000114_run.m

@@ -8,8 +8,8 @@
 
 % The directory where the data are located
 root_dir = fileparts(mfilename('fullpath'));
-bids_dir = fullfile(root_dir, 'inputs', 'ds000114');
-output_dir = fullfile(root_dir, 'outputs', 'ds000114', 'derivatives');
+bids_dir = fullfile(root_dir, 'inputs', 'ds001734');
+output_dir = fullfile(root_dir, 'outputs', 'ds001734', 'derivatives');
 
 % to say which T1w file should be used as reference
 opt.bidsFilterFile.t1w.ses = 'retest';
@@ -18,8 +18,8 @@
 
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {'01', '02'}, ...
-       'action', 'preprocess', ...
-       'task', {'linebisection'}, ...
+       'action', 'smooth', ...
+       'task', {'MGT'}, ...
        'ignore', {'unwarp', 'slicetiming'}, ...
        'space', {'IXI549Space'}, ...
        'options', opt);
@@ -41,7 +41,6 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'action', 'stats', ...
        'participant_label', {'01', '02'}, ...
-       'ignore', {'slicetiming'}, ...
        'preproc_dir', preproc_dir, ...
        'model_file', model_file, ...
        'options', opt);

demos/openneuro/ds001168_run.m

@@ -45,7 +45,6 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'action', 'stats', ...
        'participant_label', {'01'}, ...
-       'ignore', {'slicetiming'}, ...
        'preproc_dir', preproc_dir, ...
        'model_file', model_file, ...
        'keep_residuls', true);

demos/openneuro/ds001734_run.m

@@ -0,0 +1,45 @@
+%
+% Analysis of the NARPS dataset
+%
+% (C) Copyright 2022 bidspm developers
+
+clear;
+clc;
+
+addpath(fullfile(pwd, '..', '..'));
+bidspm();
+
+% The directory where the data are located
+root_dir = fileparts(mfilename('fullpath'));
+bids_dir = fullfile(root_dir, 'inputs', 'ds001734');
+fmriprep_dir =  fullfile(root_dir, 'inputs', 'ds001734-fmriprep');
+output_dir = fullfile(root_dir, 'outputs', 'ds001734', 'derivatives');
+
+subject_label = {'001'};
+task = {'MGT'};
+space = {'MNI152NLin2009cAsym'};
+
+% bidspm(fmriprep_dir, output_dir, 'subject', ...
+%        'action', 'smooth', ...
+%        'participant_label', subject_label, ...
+%        'task', task, ...
+%        'space', space, ...
+%        'fwhm', 8);
+
+%% Statistics
+
+preproc_dir = fullfile(root_dir, 'outputs', 'ds001734', 'derivatives', 'bidspm-preproc');
+model_file = fullfile(root_dir, 'models', 'model-narps_desc-U26C_smdl.json');
+
+%% Subject level analysis
+
+bidspm(bids_dir, output_dir, 'subject', ...
+       'action', 'stats', ...
+       'participant_label', subject_label, ...
+       'preproc_dir', preproc_dir, ...
+       'model_file', model_file, ...
+       'ignore', {'slice_timing'}, ...
+       'skip_validation', true, ...
+       'verbosity', 1, ...
+       'space', space, ...
+       'fwhm', 8);