[INFRA] use lighter dataset in circle ci

.circleci/config.yml

@@ -49,20 +49,20 @@ jobs:
         keys:
         - my_cache
     - run:
-        name: Get ds001734
+        name: Get ds000001
         command: |
           # Git set up: to keep datalad warnings away
           git config --global --add user.name "Ford Escort"
           git config --global --add user.email 42@H2G2.com
           mkdir -p ${HOME}/data/
-          datalad install -s ///openneuro/ds001734 ${HOME}/data/ds001734
-          datalad install -s ///openneuro-derivatives/ds001734-fmriprep ${HOME}/data/ds001734-fmriprep
-          cd ${HOME}/data/ds001734-fmriprep/
-          datalad get sub-00[1-2]/anat/*MNI152NLin2009cAsym*mask.nii.gz \
-                sub-00[1-2]/anat/*MNI152NLin2009cAsym*T1w.nii.gz \
-                sub-00[1-2]/func/*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz \
+          datalad install -s ///openneuro/ds000001 ${HOME}/data/ds000001
+          datalad install -s ///openneuro-derivatives/ds000001-fmriprep ${HOME}/data/ds000001-fmriprep
+          cd ${HOME}/data/ds000001-fmriprep/
+          datalad get sub-0[1-2]/anat/*MNI*mask.nii.gz \
+                sub-0[1-2]/anat/*MNI*T1w.nii.gz \
+                sub-0[1-2]/func/*MNI*desc-preproc*bold.nii.gz \
                 sub-*/func/*tsv	\
-                sub-*/func/*json
+                sub-*/func/*json -J 12
           datalad status
     - save_cache:
         key: my_cache
@@ -71,8 +71,8 @@ jobs:
     - persist_to_workspace:
         root: /home/circleci
         paths:
-        - data/ds001734
-        - data/ds001734-fmriprep
+        - data/ds000001
+        - data/ds000001-fmriprep
 
   test:
     machine:
@@ -83,15 +83,15 @@ jobs:
         at: /tmp/workspace
     - run: docker load -i /tmp/workspace/docker/image.tar
 
-    - run: mkdir -p ${HOME}/outputs/ds001734/derivatives
+    - run: mkdir -p ${HOME}/outputs/ds000001/derivatives
 
     - run:
         name: print version
         command: |
           user_name=cpplab
           repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
           docker run -ti --rm \
-            -v /tmp/workspace/data/ds001734:/bids_dataset \
+            -v /tmp/workspace/data/ds000001:/bids_dataset \
               ${user_name}/${repo_name} --version
 
     - run:
@@ -100,15 +100,15 @@ jobs:
           user_name=cpplab
           repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
           docker run -ti --rm \
-            -v /tmp/workspace/data/ds001734-fmriprep:/bids_dataset \
+            -v /tmp/workspace/data/ds000001-fmriprep:/bids_dataset \
             -v ${HOME}/outputs:/outputs \
               ${user_name}/${repo_name} \
                 /bids_dataset \
-                /outputs/ds001734 \
+                /outputs/ds000001 \
                 subject \
                 --action smooth \
-                --task MGT \
-                --participant_label 001 002 \
+                --task balloonanalogrisktask \
+                --participant_label 01 02 \
                 --space MNI152NLin2009cAsym \
                 --fwhm 8 \
                 --verbosity 2
@@ -123,20 +123,21 @@ jobs:
           user_name=cpplab
           repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
           docker run -ti --rm  \
-            -v /tmp/workspace/data/ds001734:/bids_dataset \
+            -v /tmp/workspace/data/ds000001:/bids_dataset \
             -v ${HOME}/outputs:/outputs \
             -v ~/project/demos/openneuro/models:/models \
               ${user_name}/${repo_name} \
                 /bids_dataset \
-                /outputs/ds001734 \
+                /outputs/ds000001 \
                 subject \
                 --action stats \
-                --preproc_dir /outputs/ds001734/derivatives/bidspm-preproc \
-                --model_file /models/model-narps_desc-U26C_smdl.json \
+                --preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
+                --model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
                 --ignore slicetiming \
+                --space MNI152NLin2009cAsym \
                 --skip_validation \
                 --fwhm 8 \
-                --participant_label 001 002 \
+                --participant_label 01 02 \
                 --verbosity 2
         no_output_timeout: 6h
 

CHANGELOG.md

@@ -28,16 +28,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-* [REF] Refactor and update CLI (#1096) @Remi-Gau
+* [REF] Refactor and update CLI in #1096 @Remi-Gau
 
 ### Deprecated
 
 ### Removed
 
-* [REF] Remove old CLI (#1096) @Remi-Gau
+* [REF] Remove old CLI in #1096 @Remi-Gau
 
 ### Fixed
 
+* [INFRA] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau
+
 ### Security
 
 

bidspm.m

@@ -28,16 +28,16 @@
     else
       bugReport(opt, ME);
     end
-    returnCode = 1;
+    rethrow(ME);
   end
 end
 
 function returnCode = executeAction(varargin)
 
-  returnCode = 0;
-
   action = varargin{1};
 
+  returnCode = 0;
+
   switch lower(action)
 
     case 'init'
@@ -278,8 +278,6 @@ function uninitBidspm()
 
   % (C) Copyright 2019 bidspm developers
 
-  % Elapsed time is 284 seconds.
-
   tic;
 
   bidspm('action', 'dev');

demos/MoAE/moae_fmriprep.m

@@ -22,34 +22,37 @@
 addpath(fullfile(pwd, '..', '..'));
 bidspm();
 
-% Getting the raw dataset to get the events.tsv
 download_data = true;
+smooth = true;
+
+% Getting the raw dataset to get the events.tsv
 download_moae_ds(download_data);
 
 %%
 subject_label = {'01'};
 task = {'auditory'};
 space = {'MNI152NLin6Asym'};
 
-%% Copy and smooth
-%
-% fmriprep data is not smoothed so we need to do that first
-%
-
 WD = fileparts(mfilename('fullpath'));
-
 bids_dir = fullfile(WD, 'inputs', 'raw');
 fmriprep_dir = fullfile(WD, 'inputs', 'fmriprep');
 
 % we need to specify where the smoothed data will go
 output_dir = fullfile(WD, 'outputs', 'derivatives');
 
-bidspm(fmriprep_dir, output_dir, 'subject', ...
-       'action', 'smooth', ...
-       'participant_label', subject_label, ...
-       'task', task, ...
-       'space', space, ...
-       'fwhm', 8);
+%% Copy and smooth
+%
+% fmriprep data is not smoothed so we need to do that first
+%
+
+if smooth
+  bidspm(fmriprep_dir, output_dir, 'subject', ...
+         'action', 'smooth', ...
+         'participant_label', subject_label, ...
+         'task', task, ...
+         'space', space, ...
+         'fwhm', 8);
+end
 
 %% STATS
 

demos/openneuro/Makefile

@@ -21,7 +21,8 @@ data_ds000001:
 	cd inputs/ds000001 && datalad get sub-0[123] -J 3
 	cd inputs/ds000001-fmriprep && datalad get sub-0[123]/func/*tsv -J 12
 	cd inputs/ds000001-fmriprep && datalad get sub-0[123]/func/*json -J 12
-	cd inputs/ds000001-fmriprep && datalad get sub-0[123]/func/*MNI*desc-*AROMA*bold.nii.gz -J 12
+	cd inputs/ds000001-fmriprep && datalad get sub-0[123]/func/*MNI*desc-*bold.nii.gz -J 12
+	cd inputs/ds000001-fmriprep && datalad get sub-0[123]/anat/*MNI*desc-preproc*.nii.gz -J 12
 
 
 data_ds000114:

demos/openneuro/ds000001_run.m

@@ -33,11 +33,13 @@
          'action', 'stats', ...
          'participant_label', participant_label(i_participant), ...
          'preproc_dir', preproc_dir, ...
+         'space', {'IXI549Space'}, ...
          'model_file', model_file);
 end
 
 %% dataset level
 bidspm(bids_dir, output_dir, 'dataset', ...
        'action', 'stats', ...
        'preproc_dir', preproc_dir, ...
+       'space', {'IXI549Space'}, ...
        'model_file', model_file);

demos/openneuro/ds000001_smooth_run.m

@@ -0,0 +1,46 @@
+% (C) Copyright 2020 bidspm developers
+%
+% shows how to smooth files from fmriprep to run a first level
+%
+
+clear;
+clc;
+
+SMOOTH = true;
+
+addpath(fullfile(pwd, '..', '..'));
+bidspm();
+
+% The directory where the data are located
+root_dir = fileparts(mfilename('fullpath'));
+bids_dir = fullfile(root_dir, 'inputs', 'ds000001');
+fmriprep_dir =  fullfile(root_dir, 'inputs', 'ds000001-fmriprep');
+output_dir = fullfile(root_dir, 'outputs', 'ds000001', 'derivatives');
+
+participant_label = {'02', '03'};
+task = {'balloonanalogrisktask'};
+space = {'MNI152NLin2009cAsym'};
+
+%% Copy preprocessed data
+if SMOOTH
+  bidspm(fmriprep_dir, output_dir, 'subject', ...
+         'action', 'smooth', ...
+         'participant_label', participant_label, ...
+         'task', task, ...
+         'space', space, ...
+         'verbosity', 3);
+end
+
+%% Stats
+preproc_dir = fullfile(root_dir, 'outputs', 'ds000001', 'derivatives', 'bidspm-preproc');
+
+model_file = fullfile(root_dir, 'models', 'model-balloonanalogrisktaskDefault_smdl.json');
+
+%% subject level
+bidspm(bids_dir, output_dir, 'subject', ...
+       'action', 'stats', ...
+       'participant_label', participant_label, ...
+       'preproc_dir', preproc_dir, ...
+       'task', task, ...
+       'space', space, ...
+       'model_file', model_file);

demos/openneuro/models/model-balloonanalogrisktaskDefault_smdl.json

@@ -5,9 +5,6 @@
   "Input": {
     "task": [
       "balloonanalogrisktask"
-    ],
-    "space": [
-      "IXI549Space"
     ]
   },
   "Nodes": [

src/IO/saveAndRunWorkflow.m

@@ -1,4 +1,4 @@
-function status = saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel)
+function [status, output] = saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel)
   %
   % Saves the SPM matlabbatch and runs it
   %
@@ -28,13 +28,14 @@
   end
 
   status = true;
+  output = {};
 
   if ~isempty(matlabbatch)
 
     saveMatlabBatch(matlabbatch, batchName, opt, subLabel);
 
     if ~opt.dryRun
-      spm_jobman('run', matlabbatch);
+      output = spm_jobman('run', matlabbatch);
     else
       status = false;
     end

src/batches/preproc/setBatchSmoothingFunc.m

@@ -1,4 +1,4 @@
-function matlabbatch = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel)
+function [matlabbatch, allRT] = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch to smooth the bold files of a subject
   %
@@ -42,24 +42,38 @@
   [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
 
   allFiles = [];
+  allRT = [];
 
   for iSes = 1:nbSessions
 
     [runs, nbRuns] = getInfo(BIDS, subLabel, opt, 'Runs', sessions{iSes});
 
     for iRun = 1:nbRuns
 
-      [fileName, subFuncDataDir] = getBoldFilename(BIDS, ...
-                                                   subLabel, sessions{iSes}, runs{iRun}, opt);
+      [fileName, subFuncDataDir, metadata] = getBoldFilename(BIDS, ...
+                                                             subLabel, ...
+                                                             sessions{iSes}, ...
+                                                             runs{iRun}, ...
+                                                             opt);
+      if isstruct(metadata)
+        metadata = {metadata};
+      end
 
-      % TODO remove this extra check
       for iFile = 1:size(fileName, 1)
-        files{iFile, 1} = validationInputFile(subFuncDataDir(iFile, :), fileName(iFile, :));
+        files{iFile, 1} = validationInputFile(subFuncDataDir(iFile, :), ...
+                                              fileName(iFile, :)); %#ok<*AGROW>
+
+        if isfield(metadata{iFile, 1}, 'RepetitionTime')
+          allRT = metadata{iFile, 1}.RepetitionTime;
+        else
+          allRT = nan;
+        end
+
       end
 
       % add the files to list
       allFilesTemp = cellstr(char(files));
-      allFiles = [allFiles; allFilesTemp]; %#ok<AGROW>
+      allFiles = [allFiles; allFilesTemp];
 
     end
   end
@@ -69,6 +83,7 @@
                                   opt, ...
                                   allFiles, ...
                                   opt.fwhm.func, ...
-                                  [spm_get_defaults('smooth.prefix'), num2str(opt.fwhm.func)]);
+                                  [spm_get_defaults('smooth.prefix'), ...
+                                   num2str(opt.fwhm.func)]);
 
 end

src/bids/getBoldFilename.m

@@ -1,4 +1,4 @@
-function [boldFilename, subFuncDataDir] = getBoldFilename(varargin)
+function [boldFilename, subFuncDataDir, metadata] = getBoldFilename(varargin)
   %
   % Get the filename and the directory of a bold file for a given session /
   % run.
@@ -66,4 +66,11 @@
   boldFilename = spm_file(fullPathBoldFilename, 'filename');
   subFuncDataDir = spm_file(fullPathBoldFilename, 'path');
 
+  metadata = getInfo(BIDS, ...
+                     subLabel, ...
+                     opt, ...
+                     'metadata', ...
+                     sessionID, ...
+                     runID, opt.bidsFilterFile.bold.suffix);
+
 end