[FIX] ensure that setBatchCoregistrationFuncToAnat takes into accou…

…nt bids_filter (#1295)

* make sure setBatchCoregistration takes bids filter into account

* minor side fixes

* update changelog

.circleci/config.yml

@@ -158,8 +158,6 @@ jobs:
                           --space IXI549Space \
                           --verbosity 3
 
-                    cat /home/circleci/outputs
-
         -   store_artifacts:
                 path: /home/circleci/outputs
 

CHANGELOG.md

@@ -58,6 +58,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter #1295 by @d-ni374
 * [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level #1248 by @d-ni374
 * [FIX] make {func}`getAcquisitionTime` less brittle #1248 by @d-ni374
 * [FIX] fix regular expression in {func}`bidsResults` to identify contrasts #1248 by @d-ni374 and #1275 by @Remi-Gau

WIP/write_model_graph.py

@@ -2,9 +2,11 @@
 
 from bids.modeling.statsmodels import BIDSStatsModelsGraph
 
+root_dir = Path("/home/remi/github/cpp-lln-lab/bidspm")
+
 graph = BIDSStatsModelsGraph(
-    layout=Path("/home/remi/github/cpp-lln-lab/bidspm/demos/MoAE/inputs/raw"),
-    model="/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/models/model-narps_desc-U26C_smdl.json",
+    layout=root_dir / "demos/MoAE/inputs/raw",
+    model=root_dir / "demos/openneuro/models/model-narps_desc-U26C_smdl.json",
 )
 
 

demos/openneuro/Makefile

@@ -25,6 +25,12 @@ data_ds000001:
 	cd inputs/ds000001-fmriprep && datalad get sub-0[1-5]/func/*MNI*desc-preproc*.nii.gz -J 12
 	cd inputs/ds000001-fmriprep && datalad get sub-0[1-3]/func/*MNI*desc-*bold.nii.gz -J 12
 
+data_ds000114_raw:
+	mkdir -p inputs
+	cd inputs && datalad install ///openneuro/ds000114
+	cd inputs/ds000114 && datalad get sub-0[1-2]/ses-*/anat/*T1w*.nii.gz -J 12
+	cd inputs/ds000114 && datalad get sub-0[1-2]/ses-*/func/*linebisection* -J 12
+
 data_ds000114:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds000114
@@ -45,11 +51,11 @@ data_ds000224:
 	cd inputs/ds000224-fmriprep && datalad get sub-MSC0[1-2]/ses-*/func/*glasslexical*MNI*_mask.nii.gz -J 12
 	cd inputs/ds000224-fmriprep && datalad get sub-MSC0[1-2]/ses-*/func/*glasslexical*MNI*desc-preproc*bold.nii.gz -J 12
 
-
 data_ds001168:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds001168
-	cd inputs/ds001168 && datalad get ds001168/sub-0[12] -J 2
+	cd inputs/ds001168 && datalad get sub-0[12]/ses*/anat/*T1w* -J 2
+	cd inputs/ds001168 && datalad get sub-0[12]/ses*/func/*fullbrain*bold* -J 2
 
 data_ds001734:
 	mkdir -p inputs

demos/openneuro/ds000114_preproc_run.m

@@ -0,0 +1,36 @@
+% (C) Copyright 2023 bidspm developers
+
+clear;
+clc;
+
+addpath(fullfile(pwd, '..', '..'));
+bidspm();
+
+participant_label = {'01'};
+TASK = 'linebisection';
+
+root_dir = fileparts(mfilename('fullpath'));
+bids_dir = fullfile(root_dir, 'inputs', 'ds000114');
+output_dir = fullfile(root_dir, 'outputs', 'ds000114', 'derivatives');
+preproc = fullfile(output_dir, 'bidspm-preproc');
+
+bidspm(bids_dir, output_dir, 'subject', ...
+       'participant_label', participant_label, ...
+       'action', 'copy', ...
+       'task', TASK, ...
+       'skip_validation', true, ...
+       'verbosity', 3);
+
+bids_filter_file = struct( ...
+                          'bold', struct('modality', 'func', 'suffix', 'bold', 'ses', 'retest'), ...
+                          't1w',  struct('modality', 'anat', 'suffix', 'T1w'));
+bidspm(bids_dir, output_dir, 'subject', ...
+       'participant_label', participant_label, ...
+       'action', 'preprocess', ...
+       'task', TASK, ...
+       'space', {'IXI549Space'}, ...
+       'skip_validation', true, ...
+       'ignore', {'slicetiming', 'unwarp'}, ...
+       'bids_filter_file', bids_filter_file, ...
+       'fwhm', 6, ...
+       'verbosity', 3);

demos/openneuro/ds001168_run.m

@@ -38,7 +38,8 @@
        'action', 'preprocess', ...
        'task', 'rest', ...
        'space', {'IXI549Space'}, ...
-       'ignore', {'slicetiming'}, ...
+       'skip_validation', true, ...
+       'ignore', {'slicetiming', 'fieldmaps'}, ...
        'options', opt);
 
 %% denoise with GLM
@@ -50,5 +51,6 @@
        'action', 'stats', ...
        'participant_label', {'01'}, ...
        'preproc_dir', preproc_dir, ...
+       'skip_validation', true, ...
        'model_file', model_file, ...
        'keep_residuls', true);

src/batches/preproc/setBatchCoregistrationFuncToAnat.m

@@ -56,6 +56,8 @@
 
   % OTHER IMAGES : DEPENDENCY FROM REALIGNEMENT
 
+  opt.query = opt.bidsFilterFile.bold;
+
   [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
 
   runCounter = 1;

tests/tests_batches/preproc/test_setBatchCoregistrationFuncToAnat.m

@@ -56,6 +56,40 @@ function test_setBatchCoregistrationFuncToAnat_basic()
 
 end
 
+function test_setBatchCoregistrationFuncToAnat_one_session()
+
+  subLabel = '01';
+
+  opt = setOptions('vismotion', subLabel);
+
+  opt.bidsFilterFile.bold.ses = '02';
+
+  BIDS = getLayout(opt);
+
+  opt.orderBatches.selectAnat = 1;
+  opt.orderBatches.realign = 2;
+
+  matlabbatch = {};
+  matlabbatch = setBatchCoregistrationFuncToAnat(matlabbatch, BIDS, opt, subLabel);
+
+  nbRuns = 2;
+
+  meanImageToUse = 'meanuwr';
+  otherImageToUse = 'uwrfiles';
+
+  expectedBatch = returnExpectedBatch(nbRuns, meanImageToUse, otherImageToUse);
+  assertEqual( ...
+              matlabbatch{1}.spm.spatial.coreg.estimate.ref, ...
+              expectedBatch{1}.spm.spatial.coreg.estimate.ref);
+  assertEqual( ...
+              matlabbatch{1}.spm.spatial.coreg.estimate.source, ...
+              expectedBatch{1}.spm.spatial.coreg.estimate.source);
+  assertEqual( ...
+              matlabbatch{1}.spm.spatial.coreg.estimate.other, ...
+              expectedBatch{1}.spm.spatial.coreg.estimate.other);
+
+end
+
 function test_setBatchCoregistrationFuncToAnat_no_unwarp()
 
   subLabel = '01';