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Merged
Remi-Gau merged 2 commits into from
Sep 19, 2023
Merged

[ENH] allow to run substeps of bms #1145

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6178dd3
allow to run substeps of bms
Remi-Gau Sep 19, 2023
02a9d91
update changelog
Remi-Gau Sep 19, 2023
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9 changes: 6 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -24,7 +24,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added

* [ENH] Add several confound strategies to add to bids stats model and a function to create family of models #1126 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
* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit several other information criteria (AIC, BIC) #1135 by @Remi-Gau
* [ENH] add several confound strategies to add to bids stats model and a function to create family of models #1126 by @Remi-Gau
* [ENH] add CLI to run bayesian model selection #1121 by @Remi-Gau
* [ENH] support label of activations with all atlases [1100](https://github.com/cpp-lln-lab/bidspm/pull/1100) by [Remi-Gau](https://github.com/Remi-Gau)
* [ENH] add support for session level models #1116 be @Remi-Gau
Expand Down Expand Up @@ -77,7 +80,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* [ENH] make it possible to update bidspm from any folder in [948](https://github.com/cpp-lln-lab/bidspm/pull/948) by [Remi-Gau](https://github.com/Remi-Gau)
* [ENH] use filtering of layout in [944](https://github.com/cpp-lln-lab/bidspm/pull/944) by [Remi-Gau](https://github.com/Remi-Gau)
* [ENH] make reports more silent in [939](https://github.com/cpp-lln-lab/bidspm/pull/939) by [Remi-Gau](https://github.com/Remi-Gau)
* [ENH] Add CC0 license by default to all outputs in [898](https://github.com/cpp-lln-lab/bidspm/pull/898) by [Remi-Gau](https://github.com/Remi-Gau)
* [ENH] add CC0 license by default to all outputs in [898](https://github.com/cpp-lln-lab/bidspm/pull/898) by [Remi-Gau](https://github.com/Remi-Gau)

### Changed

Expand All @@ -90,7 +93,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

* [FIX] Fix vismotion demo in [1070](https://github.com/cpp-lln-lab/bidspm/pull/1070) by [Remi-Gau](https://github.com/Remi-Gau)
* [FIX] fix vismotion demo in [1070](https://github.com/cpp-lln-lab/bidspm/pull/1070) by [Remi-Gau](https://github.com/Remi-Gau)
* [FIX] Exclude from GLM specification events with onsets longer than the run duration in [1060](https://github.com/cpp-lln-lab/bidspm/pull/1060) by [Remi-Gau](https://github.com/Remi-Gau)
* [FIX] remove dummies from preproc dataset and not raw dataset when using CLI in [1057](https://github.com/cpp-lln-lab/bidspm/pull/1057) by [Remi-Gau](https://github.com/Remi-Gau)
* [FIX] skip smoothing when running bidspm prepoc in dryRun in [1054](https://github.com/cpp-lln-lab/bidspm/pull/1054) by [Remi-Gau](https://github.com/Remi-Gau)
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6 changes: 4 additions & 2 deletions bidspm.m
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Expand Up @@ -85,7 +85,7 @@
case {'stats', 'contrasts', 'results', 'specify_only'}
cliStats(varargin{2:end});

case {'bms'}
case {'bms', 'bms-posterior', 'bms-bms'}
cliBayesModel(varargin{2:end});

case 'meaning_of_life'
Expand Down Expand Up @@ -375,7 +375,9 @@ function update()
'contrasts'; ...
'results'; ...
'specify_only', ...
'bms'};
'bms'; ...
'bms-posterior'; ...
'bms-bms'};

end

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12 changes: 11 additions & 1 deletion demos/bayes/Makefile
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@@ -1,11 +1,21 @@
.PHONY: clean data data_ds000001

data_ds000114:
data_install:
mkdir -p inputs
cd inputs && datalad install ///openneuro/ds000114
cd inputs && datalad install ///openneuro-derivatives/ds000114-fmriprep
cd inputs/ds000114-fmriprep && datalad get sub-*/anat/*MNI152NLin2009cAsym*desc-preproc*.nii.gz -J 12

data_ds000114: data_install
cd inputs/ds000114-fmriprep && datalad get sub-*/anat/*MNI152NLin2009cAsym*desc-preproc*.nii.gz -J 12
cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*tsv -J 12
cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*json -J 12
cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*overtverbgeneration*MNI152NLin2009cAsym*_mask.nii.gz -J 12
cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*overtverbgeneration*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz -J 12

data_ds000114_testing: data_install
cd inputs/ds000114-fmriprep && datalad get sub-0[12]/anat/*MNI152NLin2009cAsym*desc-preproc*.nii.gz -J 12
cd inputs/ds000114-fmriprep && datalad get sub-0[12]/ses-*/func/*tsv -J 12
cd inputs/ds000114-fmriprep && datalad get sub-0[12]/ses-*/func/*json -J 12
cd inputs/ds000114-fmriprep && datalad get sub-0[12]/ses-*/func/*overtverbgeneration*MNI152NLin2009cAsym*_mask.nii.gz -J 12
cd inputs/ds000114-fmriprep && datalad get sub-0[12]/ses-*/func/*overtverbgeneration*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz -J 12
55 changes: 51 additions & 4 deletions demos/bayes/ds000114_run.m
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Expand Up @@ -6,7 +6,7 @@
addpath(fullfile(pwd, '..', '..'));
bidspm();

VERBOSITY = 2;
VERBOSITY = 0;

FWHM = 8;

Expand All @@ -16,6 +16,9 @@
% set to false to not re run the model specification
FIRST_LEVEL = true;

% set to false to not compute cross-validated log model evidence
CVLME = true;

% set to true to run on fewer subjects and fewer models
TESTING = true;

Expand Down Expand Up @@ -46,7 +49,7 @@
'options', opt); %#ok<*UNRCH>
end

%% create models from a default one
%% create models family from a default one

default_model_file = fullfile(models_dir, 'default_model.json');

Expand All @@ -66,7 +69,7 @@
%% Statistics
preproc_dir = fullfile(output_dir, 'bidspm-preproc');

%% Subject level analysis
% Subject level analysis
if FIRST_LEVEL

% Silence this warning as this dataset has not been slice time corrected.
Expand All @@ -84,8 +87,52 @@

end

% Run bayesian model selection
% 1. MA_model_space: defines a model space
% 2. MA_cvLME_auto: computes cross-validated log model evidence
% 3. MS_PPs_group_auto: calculate posterior probabilities from cvLMEs
% 4. MS_BMS_group_auto: perform cross-validated Bayesian model selection
% 5. MS_SMM_BMS: generate selected models maps from BMS
if CVLME

bidspm(bids_dir, output_dir, 'subject', ...
'action', 'bms', ...
'participant_label', participant_label, ...
'models_dir', models_dir, ...
'fwhm', FWHM, ...
'skip_validation', true, ...
'verbosity', VERBOSITY);

end

%% Redefine the model space
% note that it must be a subset of the one defined previously
clear multiverse;
delete(fullfile(pwd, 'models', 'model*.json'));

multiverse.motion = {'basic', 'full'};
multiverse.scrub = {false};
multiverse.non_steady_state = {true};

createModelFamilies(default_model_file, multiverse, models_dir);

%%
% Runs a new bayesian model selection
% but rely on CVLME estimated previously
% 1. MA_model_space: defines a model space
% 2. MS_PPs_group_auto: calculate posterior probabilities from cvLMEs
bidspm(bids_dir, output_dir, 'subject', ...
'action', 'bms-posterior', ...
'participant_label', participant_label, ...
'models_dir', models_dir, ...
'fwhm', FWHM, ...
'skip_validation', true, ...
'verbosity', VERBOSITY);

% 3. MS_BMS_group_auto: perform cross-validated Bayesian model selection
% 4. MS_SMM_BMS: generate selected models maps from BMS
bidspm(bids_dir, output_dir, 'subject', ...
'action', 'bms', ...
'action', 'bms-bms', ...
'participant_label', participant_label, ...
'models_dir', models_dir, ...
'fwhm', FWHM, ...
Expand Down
10 changes: 9 additions & 1 deletion src/cli/cliBayesModel.m
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Expand Up @@ -18,13 +18,21 @@ function cliBayesModel(varargin)

validate(args);

action = args.Results.action;
opt = getOptionsFromCliArgument(args);
opt.pipeline.type = 'stats';
opt.pipeline.isBms = true;
opt = checkOptions(opt);

saveOptions(opt);

bidsModelSelection(opt, 'action', 'all');
switch action
case 'bms'
bidsModelSelection(opt, 'action', 'all');
case 'bms-posterior'
bidsModelSelection(opt, 'action', 'posterior');
case 'bms-bms'
bidsModelSelection(opt, 'action', 'BMS');
end

end
7 changes: 5 additions & 2 deletions src/cli/getOptionsFromCliArgument.m
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Expand Up @@ -70,7 +70,7 @@

opt = optionsStats(opt, args, action);

if ismember(lower(action), {'bms'})
if ismember(lower(action), {'bms', 'bms-posterior', 'bms-bms'})
opt.toolbox.MACS.model.dir = args.Results.models_dir;
end

Expand Down Expand Up @@ -140,7 +140,10 @@
'contrasts'; ...
'results'; ...
'specify_only'; ...
'bms'};
'bms'; ...
'bms-posterior'; ...
'bms-bms' ...
};
end

function opt = getOptions(args)
Expand Down
1 change: 0 additions & 1 deletion src/cli/inputParserForBayesModel.m
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Expand Up @@ -10,7 +10,6 @@
isLogical = @(x) islogical(x) && numel(x) == 1;
isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
isFolder = @(x) isdir(x);
isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x); %#ok<*ISCLSTR>

addParameter(args, 'models_dir', pwd, isFolder);

Expand Down
10 changes: 10 additions & 0 deletions src/messages/bidspmHelp.m
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Expand Up @@ -388,6 +388,16 @@ function bidspmHelp()
% 'dry_run', false, ...
% 'skip_validation', false)
%
% :param action: Any of: ``{'bms', 'bms-posterior', 'bms-bms'}``
% `'bms'` will performm all steps for the baeysian
% model selection. If `'bms'` has been performed
% than ``'bms-posterior'`` can``'bms-bms'``
% be performed one aftr the other set a new model
% space and perform bayesian model selection on it.
% See the help section of :func:`bidsModelSelection`
% for more details.
% :type action: char
%
% :param models_dir: A path to a dir can be passed as well.
% In this case all ``*_smdl.json`` files will be used
% and looped over.
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3 changes: 0 additions & 3 deletions tests/tests_slow/tests_workflows/stats/test_bidsModelSelection.m
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@@ -1,8 +1,5 @@
function test_suite = test_bidsModelSelection %#ok<*STOUT>
%

% (C) Copyright 2022 bidspm developers

try % assignment of 'localfunctions' is necessary in Matlab >= 2016
test_functions = localfunctions(); %#ok<*NASGU>
catch % no problem; early Matlab versions can use initTestSuite fine
Expand Down