[FIX] Remove goodness of fit for dataset level and update container definitions (#1265)

* misc fix

* rm GoF for dataset level

* install java

* add zip

* update changelog

* add unzip

* fix tests

Author: Remi-Gau

.circleci/config.yml

@@ -202,6 +202,7 @@ jobs:
                           --space MNI152NLin2009cAsym \
                           --skip_validation \
                           --fwhm 0 \
+                          --participant_label 01 02 \
                           --verbosity 3 \
                           --options /options/ds000001.json
 

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+* [ENH] add Apptainer definition #1254 by @Remi-Gau and @monique2208
 * [ENH] allow to copy anat only on raw datasets #1181 by @Remi-Gau
 * [ENH] add option to concatenate runs at subject level to facilite running PPI analysis #1133 by @Remi-Gau
 * [ENH] allow to run substeps of substeps of the bayesian model selection #1145 by @Remi-Gau
@@ -40,7 +41,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+* [DOC] change theme and structure of the documentation #1256 @Remi-Gau
 * [REF] Refactor and update CLI in #1096 @Remi-Gau
+* [ENH] {func}`getData` only loads anat data when requested #1257 @Remi-Gau
 
 ### Deprecated
 
@@ -50,12 +53,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [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
+* [FIX] pass analysis level to stats actions when using python CLI #1258 @Remi-Gau
+* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox #1265 by @Remi-Gau
+* [FIX] add java and zip to container recipes to allow using nidm results with octave #1265 by @Remi-Gau
 * [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation #1203 by @Remi-Gau
-* [FIX] save onsets.mat directly in subject stats folder #1187 by @Remi-Gau
+* [FIX] save `onsets.mat` directly in subject stats folder #1187 by @Remi-Gau
 * [FIX] do not compute subject level contrast when running dataset level #1102 by @Remi-Gau
 * [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau
 * [FIX] rename results files (csv, tsv, png, nii) of each contrasts #1104 by @Remi-Gau
-* [DIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau
+* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau
 
 ### Security
 

Dockerfile

@@ -5,25 +5,28 @@ ARG DEBIAN_FRONTEND="noninteractive"
 ## basic OS tools install octave
 RUN apt-get update -qq && \
     apt-get -qq -y --no-install-recommends install \
-        build-essential \
-        software-properties-common \
         apt-utils \
+        build-essential \
         ca-certificates \
-        git \
         curl \
-        python3 \
-        python3-pip \
+        default-jre \
         fonts-freefont-otf \
         ghostscript \
+        git \
         gnuplot-x11 \
         libcurl4-gnutls-dev \
-        octave \
         liboctave-dev \
+        octave \
         octave-common \
         octave-io \
         octave-image \
         octave-signal \
-        octave-statistics && \
+        octave-statistics \
+        python3-pip \
+        python3 \
+        software-properties-common \
+        unzip \
+        zip && \
     apt-get clean && \
     rm -rf \
         /tmp/hsperfdata* \
@@ -42,7 +45,6 @@ RUN mkdir /opt/spm12 && \
     make -C /opt/spm12/src PLATFORM=octave install && \
     ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
 
-
 WORKDIR /home/neuro
 
 COPY . /home/neuro/bidspm

bidspm.def

@@ -13,25 +13,28 @@ From: bids/base_validator:1.13.1
 %post
     apt-get -qq update
     DEBIAN_FRONTEND=noninteractive apt-get --yes --quiet install \
-        build-essential \
-        software-properties-common \
         apt-utils \
+        build-essential \
         ca-certificates \
-        git \
         curl \
-        python3 \
-        python3-pip \
+        default-jre \
         fonts-freefont-otf \
         ghostscript \
+        git \
         gnuplot-x11 \
         libcurl4-gnutls-dev \
-        octave \
         liboctave-dev \
+        octave \
         octave-common \
         octave-io \
         octave-image \
         octave-signal \
-        octave-statistics && \
+        octave-statistics \
+        python3-pip \
+        python3 \
+        software-properties-common \
+        unzip \
+        zip && \
     apt-get clean && \
     rm -rf \
         /tmp/hsperfdata* \

demos/openneuro/Makefile

@@ -23,7 +23,7 @@ data_ds000001:
 	cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*json -J 12
 	cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/anat/*MNI*desc-preproc*.nii.gz -J 12
 	cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-preproc*.nii.gz -J 12
-    cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-*bold.nii.gz -J 12
+	cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-*bold.nii.gz -J 12
 
 data_ds000114:
 	mkdir -p inputs

src/batches/stats/setBatchEstimateModel.m

@@ -91,7 +91,6 @@
 
         matlabbatch = returnEstimateModelBatch(matlabbatch, spmMatFile, opt);
         opt.orderBatches.estimate = numel(matlabbatch);
-        matlabbatch = setBatchGoodnessOfFit(matlabbatch, opt);
         matlabbatch = setBatchInformationCriteria(matlabbatch, opt, rfxDir);
 
         matlabbatch{end + 1}.spm.stats.review.spmmat = spmMatFile; %#ok<*AGROW>

tests/tests_slow/tests_workflows/stats/test_bidsRFX.m

@@ -19,7 +19,7 @@ function test_bidsRFX_rfx()
   % 2 dummy contrasts
   % 2 contrasts
   nbGroupLevelModels = 4;
-  nbBatchPerModel = 8;
+  nbBatchPerModel = 7;
   if bids.internal.is_octave()
     nbBatchPerModel = 5;
   end
@@ -35,7 +35,7 @@ function test_bidsRFX_rfx()
 
   % setBatchEstimateModel creates 3 batches for each model (estimate, review, figure)
   batchOrder = extendBatchOrder();
-  idx = 9:6:(nbGroupLevelModels * nbBatchPerModel);
+  idx = 9:5:(nbGroupLevelModels * nbBatchPerModel);
   if bids.internal.is_octave()
     idx = 9:3:(nbGroupLevelModels * nbBatchPerModel);
   end
@@ -57,7 +57,7 @@ function test_bidsRFX_no_overwrite_smoke_test()
 
   matlabbatch = bidsRFX('RFX', opt);
 
-  expectedNbBatch = 8;
+  expectedNbBatch = 7;
   if bids.internal.is_octave()
     expectedNbBatch = 5;
   end
@@ -80,14 +80,13 @@ function test_bidsRFX_within_group_ttest()
   if bids.internal.is_octave()
     assertEqual(numel(matlabbatch), 10);
   else
-    assertEqual(numel(matlabbatch), 16);
+    assertEqual(numel(matlabbatch), 14);
   end
 
   % creates 1 batch for
   %   - specify
   %   - figure
   %   - estimate
-  %   - MACS: goodness of fit
   %   - MACS: model space
   %   - MACS: information criteria
   %   - review
@@ -110,7 +109,7 @@ function test_bidsRFX_within_group_ttest()
                 fileparts(matlabbatch{8}.spm.stats.fmri_est.spmmat{1}));
   else
     assertEqual(matlabbatch{3}.spm.stats.factorial_design.dir{1}, ...
-                fileparts(matlabbatch{11}.spm.stats.fmri_est.spmmat{1}));
+                fileparts(matlabbatch{10}.spm.stats.fmri_est.spmmat{1}));
   end
 
 end
@@ -191,7 +190,7 @@ function test_bidsRFX_several_datasets_level()
   assertEqual(summary, batchOrder);
 
   nbGroupLevelModelsReturned = 1;
-  nbBatchPerModel = 8;
+  nbBatchPerModel = 7;
   if bids.internal.is_octave()
     nbBatchPerModel = 5;
   end
@@ -250,13 +249,12 @@ function test_bidsRFX_contrast()
     batchOrder = {};
   end
   extension = {'stats', 'fmri_est'; ...
-               'tools', 'MACS'; ... % skip on octave
                'tools', 'MACS'; ...
                'tools', 'MACS'; ...
                'stats', 'review'; ...
                'util', 'print'};
   if bids.internal.is_octave()
-    extension(2:4, :) = [];
+    extension(2:3, :) = [];
   end
   batchOrder = cat(1, batchOrder, extension);
 end