Merge pull request #584 from Remi-Gau/parametric_and_f_test

[ENH] add F test

.github/workflows/run_system_tests_matlab.yml

@@ -54,14 +54,6 @@ jobs:
       - name: Copy Macs toolbox to SPM inputs_folder
         run: cp -rv lib/MACS spm12/toolbox/MACS
 
-      - name: Prepare data
-        run: |
-          inputs_folder='demos/MoAE/inputs/'
-          mkdir $inputs_folder
-          curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
-          unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
-          mv $inputs_folder/MoAEpilot $inputs_folder/raw
-
       - name: Run commands
         uses: matlab-actions/run-command@v1.0.1
         with:

.github/workflows/system_tests_matlab.m

@@ -5,6 +5,9 @@
 
 addpath(fullfile(root_dir, 'spm12'));
 
+cd demos/MoAE;
+download_moae_ds(true);
+
 cd(fullfile(root_dir, 'manualTests'));
 
 run test_moae;

README.md

@@ -1,5 +1,7 @@
 <!-- markdown-link-check-disable -->
 
+<!-- .. only:: html -->
+
 [![Documentation Status: stable](https://readthedocs.org/projects/cpp_spm/badge/?version=stable)](https://cpp_spm.readthedocs.io/en/stable/?badge=stable)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_SPM/dev)
 [![miss_hit_quality](https://github.com/cpp-lln-lab/CPP_SPM/actions/workflows/miss_hit_quality.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_SPM/actions/workflows/miss_hit_quality.yml)
@@ -102,8 +104,8 @@ filenames.
 ### Statistics
 
 The model specification are set up using the
-[BIDS stats model](https://bids-standard.github.io/stats-models/intro.html) and
-can be used to perform:
+[BIDS stats model](https://bids-standard.github.io/stats-models/) and can be
+used to perform:
 
 -   whole GLM at the subject level
 -   whole brain GLM at the group level à la SPM (meaning using a summary

cpp_spm.m

@@ -479,7 +479,7 @@ function detectCppSpm()
     for i = 1:numel(workflowsDir)
       fprintf('  * %s\n', fullfile(workflowsDir{i}, '..', '..'));
     end
-    error('Remove all but one with ''pathtool''' .\ n'); % or ''spm_rmpath
+    error('Remove all but one with ''pathtool''.\n'); % or ''spm_rmpath
 
   end
 end

demos/face_repetition/face_rep_02_stats.m

@@ -8,8 +8,6 @@
 % (C) Copyright 2019 Remi Gau
 
 % TODO
-% - compute the relevant contrasts
-% - compute motion effect
 % - run parametric model
 
 clear;
@@ -21,7 +19,7 @@
 opt = face_rep_get_option_results();
 opt.space = 'IXI549Space';
 
-bidsFFX('specifyAndEstimate', opt);
+% bidsFFX('specifyAndEstimate', opt);
 bidsFFX('contrasts', opt);
 
 bidsResults(opt);

demos/face_repetition/face_rep_get_option_results.m

@@ -16,6 +16,7 @@
                             'model-faceRepetition_smdl.json');
 
   % Specify the result to compute
+  opt.results = defaultResultsStructure();
   opt.results.nodeName = 'run_level';
 
   opt.results.name = 'faces_gt_baseline_1';
@@ -25,12 +26,17 @@
   opt.results.csv = true();
   opt.results.threshSpm = true();
   opt.results.binary = true();
-
-  % MONTAGE FIGURE OPTIONS
   opt.results.montage.do = true();
   opt.results.montage.slices = -26:3:6; % in mm
   opt.results.montage.orientation = 'axial';
 
+  results = defaultResultsStructure();
+  results.nodeName = 'run_level';
+  results.name = 'motion';
+  results.png = true();
+
+  opt.results(2) = results;
+
   %% DO NOT TOUCH
   opt = checkOptions(opt);
   saveOptions(opt);

demos/face_repetition/models/model-faceRepetition_smdl.json

@@ -99,6 +99,26 @@
                   -1
                ],
                "Test": "t"
+            },
+            {
+               "Name": "motion",
+               "ConditionList": [
+                  "trans_x",
+                  "trans_y",
+                  "trans_z",
+                  "rot_x",
+                  "rot_y",
+                  "rot_z"
+               ],
+               "Weights": [
+                  1,
+                  1,
+                  1,
+                  1,
+                  1,
+                  1
+               ],
+               "Test": "F"
             }
          ]
       }

docs/Makefile

@@ -12,7 +12,7 @@ BUILDDIR      = build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+.PHONY: help Makefile cpp_spm-manual.pdf
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
@@ -21,10 +21,14 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)
+	rm -f cpp_spm-manual.pdf
 clean_default_options: source/default_options.m
 	sed -i "s@/home/remi/matlab/SPM/spm12@spm12_dir@g" source/default_options.m
 	sed -i "s@/home/remi/github/CPP_SPM/docs/derivatives@derivatives@g" source/default_options.m
 	sed -i "s@/home/remi/github/CPP_SPM/docs/jobs@jobs@g" source/default_options.m
 	sed -i "s@\t@ @g" source/default_options.m
 view:
 	firefox build/html/index.html
+
+cpp_spm-manual.pdf:
+	bash create_manual.sh

docs/source/conf.py

@@ -16,15 +16,16 @@
 sys.path.insert(0, os.path.abspath("../.."))
 
 
+# The full version, including alpha/beta/rc tags
+with open('../../version.txt', encoding='utf-8') as version_file:
+    release = version_file.read()
+
 # -- Project information -----------------------------------------------------
 
 project = "CPP SPM"
 copyright = "2020, the CPP SPM pipeline dev team"
 author = "the CPP SPM pipeline dev team"
 
-# The full version, including alpha/beta/rc tags
-release = "v1.1.3dev"
-
 
 # -- General configuration ---------------------------------------------------
 
@@ -68,9 +69,9 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = ["images"]
 
-html_logo = "_static/cpp_lab_logo.png"
+html_logo = "images/cpp_lab_logo.png"
 
 html_theme_options = {
     "collapse_navigation": False,

docs/source/defaults.rst

@@ -75,5 +75,7 @@ spm to BIDS filename conversion
 list of defaults
 ================
 
-.. literalinclude:: default_options.m
-   :language: matlab
+.. only:: html
+
+    .. literalinclude:: default_options.m
+        :language: matlab

docs/source/preprocessing.rst

@@ -24,7 +24,7 @@ More info available on this page of the
 `SPM wikibook <https://en.wikibooks.org/wiki/SPM/Slice_Timing>`_.
 
 .. _fig_stc:
-.. figure::  _static/bidsSTC/out.png
+.. figure::  images/bidsSTC/out.png
    :align:   center
 
    Slice timing correction workflow
@@ -74,13 +74,13 @@ The figures below show the ``bidsSpatialPrepro`` workflow as it would run using
 realign and unwarp (default) and with normalization to SPM MNI space (``IXI549Space``).
 
 .. _fig_spatialPrepro-anat:
-.. figure::  _static/bidsSpatialPrepro/out_anat.png
+.. figure::  images/bidsSpatialPrepro/out_anat.png
    :align:   center
 
    Anatomical component of the spatial preprocessing workflow
 
 .. _fig_spatialPrepro-func:
-.. figure::  _static/bidsSpatialPrepro/out_func.png
+.. figure::  images/bidsSpatialPrepro/out_func.png
    :align:   center
 
    Functional component of the spatial preprocessing workflow
@@ -96,7 +96,7 @@ Perform smoothing of the functional data by running ``bidsSmoothing``
 .. autofunction:: bidsSmoothing
 
 .. _fig_smoothing:
-.. figure::  _static/bidsSmoothing/out.png
+.. figure::  images/bidsSmoothing/out.png
    :align:   center
 
    Smoothing workflow
@@ -108,7 +108,7 @@ Others
 .. autofunction:: bidsSegmentSkullStrip
 
 .. _fig_segmentSkullstrip:
-.. figure::  _static/bidsSegmentSkullstrip/out.png
+.. figure::  images/bidsSegmentSkullstrip/out.png
    :align:   center
 
    Segment and skullstrip workflow

docs/source/quality_analysis.rst

@@ -14,7 +14,7 @@ Quality control
 .. autofunction:: functionalQA
 
 .. _fig_spatialPrepro-reports:
-.. figure::  _static/bidsSpatialPrepro/out_report.png
+.. figure::  images/bidsSpatialPrepro/out_report.png
    :align:   center
 
    workflows for QA as part of the spatial preprocessing workflow

docs/source/statistics.rst

@@ -55,7 +55,7 @@ The mat files can directly be ingested by SPM:
 the TSV files are there for both logging and interoperability.
 
 .. _fig_FFX-specification:
-.. figure::  _static/bidsFFX/out.png
+.. figure::  images/bidsFFX/out.png
    :align:   center
 
    Subject level GLM specification workflow for model specification
@@ -72,16 +72,16 @@ Compute results
 
 .. autofunction:: bidsResults
 
-:download:`CSV output example <_static/results_fig/output.csv>`
+:download:`CSV output example <images/results_fig/output.csv>`
 
 .. _MoAE_output_figure:
-.. figure::  _static/results_fig/output.png
+.. figure::  images/results_fig/output.png
    :align:   center
 
    Example of subject level results from the MoAE demo
 
 .. _MoAE_montage_figure:
-.. figure::  _static/results_fig/montage.png
+.. figure::  images/results_fig/montage.png
    :align:   center
 
    Example of subject level montage from the MoAE demo
@@ -98,7 +98,7 @@ An example of how to use it is available in the ``moae_04_slice_display.m``
 script in the MoAE demo.
 
 .. _MoAE_slice_display_figure:
-.. figure::  _static/results_fig/slice_display.png
+.. figure::  images/results_fig/slice_display.png
    :align:   center
 
    Example of subject level slice display from the MoAE demo

src/batches/stats/setBatchContrasts.m

@@ -8,10 +8,13 @@
   %
   % :param matlabbatch:
   % :type matlabbatch: cell
+  %
   % :param opt:
   % :type opt: structure
+  %
   % :param spmMatFile:
   % :type spmMatFile: string
+  %
   % :param consess:
   % :type consess: cell
   %

src/batches/stats/setBatchGroupLevelContrasts.m

@@ -1,4 +1,23 @@
 function matlabbatch = setBatchGroupLevelContrasts(matlabbatch, opt, nodeName)
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBatchGroupLevelContrasts(matlabbatch, opt, nodeName)
+  %
+  % :param matlabbatch:
+  % :type matlabbatch: structure
+  %
+  % :param opt:
+  % :type opt: structure
+  %
+  % :param nodeName:
+  % :type nodeName: string
+  %
+  % :returns: - :matlabbatch:
+  %
+  %
+  %
+  % See also: setBatchContrasts, specifyContrasts, setBatchSubjectLevelContrasts
   %
   % (C) Copyright 2019 CPP_SPM developers
 

src/batches/stats/setBatchSubjectLevelContrasts.m

@@ -1,4 +1,4 @@
-function matlabbatch = setBatchSubjectLevelContrasts(matlabbatch, opt, subLabel)
+function matlabbatch = setBatchSubjectLevelContrasts(matlabbatch, opt, subLabel, nodeName)
   %
   % set batch for run and subject level contrasts
   %
@@ -17,6 +17,10 @@
   %
   % :returns: - :matlabbatch:
   %
+  %
+  % See also: bidsFFX, specifyContrasts, setBatchContrasts
+  %
+  %
   % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('subject level contrasts specification', opt);
@@ -31,15 +35,31 @@
   model = opt.model.bm;
 
   % Create Contrasts
-  contrasts = specifyContrasts(SPM, model);
+  if nargin < 4 || isempty(nodeName)
+    contrasts = specifyContrasts(SPM, model);
+  else
+    contrasts = specifyContrasts(SPM, model, nodeName);
+  end
 
   consess = {};
-  for icon = 1:size(contrasts, 2)
-    if any(contrasts(icon).C)
-      consess{end + 1}.tcon.name = contrasts(icon).name; %#ok<*AGROW>
-      consess{end}.tcon.convec = contrasts(icon).C;
-      consess{end}.tcon.sessrep = 'none';
+  for icon = 1:numel(contrasts)
+
+    if any(contrasts(icon).C(:))
+
+      con.name = contrasts(icon).name;
+      con.convec = contrasts(icon).C;
+      con.sessrep = 'none';
+
+      switch contrasts(icon).type
+        case 't'
+          consess{end + 1}.tcon = con; %#ok<*AGROW>
+
+        case 'F'
+          consess{end + 1}.fcon = con; %#ok<*AGROW>
+      end
+
     end
+
   end
 
   matlabbatch = setBatchContrasts(matlabbatch, opt, spmMatFile, consess);

src/batches/stats/setBatchSubjectLevelResults.m

@@ -32,7 +32,7 @@
     result.name = char(result.name);
     result.name = regexify(result.name);
 
-    msg = sprintf('Skipping contrast named "%s"', result.name(2:end - 1));
+    msg = sprintf('Skipping contrast named "%s"', deregexify(result.name));
     errorHandling(mfilename(), 'skippingContrastResults', msg, true, opt.verbosity);
     return
 
@@ -44,7 +44,7 @@
 
     msg = sprintf('\nGetting too many contrasts in SPM file\n%s\nfor the name:\n %s', ...
                   fullfile(result.dir, 'SPM.mat'), ...
-                  result.name(2:end - 1));
+                  deregexify(result.name));
     errorHandling(mfilename(), 'noMatchingContrastName', msg, true, opt.verbosity);
     return