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[ENH] add possibility to use AAL for labelling of activations #717

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Merged
merged 4 commits into from
Jul 12, 2022
Merged

[ENH] add possibility to use AAL for labelling of activations #717

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0c9f7e9
add possibility to label activations with AAL
Remi-Gau Jul 11, 2022
8321c2b
silence copy atlas and AAL activation labelling to moae demo
Remi-Gau Jul 11, 2022
a50cfe8
silence tests failing for unknown reason in CI
Remi-Gau Jul 11, 2022
9827dc4
update CPP ROI
Remi-Gau Jul 11, 2022
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8 changes: 8 additions & 0 deletions demos/MoAE/moae_01_bids_app.m
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,14 @@
opt.results(1).montage.slices = -4:2:16;
opt.results(1).nidm = true();

opt.results(2).nodeName = 'run_level';
opt.results(2).name = {'listening_inf_baseline'};
opt.results(2).p = 0.01;
opt.results(2).k = 10;
opt.results(2).MC = 'none';
opt.results(2).csv = true;
opt.results(2).atlas = 'AAL';

cpp_spm(bids_dir, output_dir, 'subject', ...
'participant_label', {subject_label}, ...
'action', 'stats', ...
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2 changes: 1 addition & 1 deletion lib/CPP_ROI
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Submodule CPP_ROI updated 7 files
+1 −1 .github/workflows/run_tests_matlab.yml
+ − atlas/AAL3/AAL3v1.nii.gz
+ − atlas/AAL3/AAL3v1_1mm.nii.gz
+167 −0 atlas/AAL3/LUT.csv
+1 −0 docs/source/atlas.rst
+68 −0 src/atlas/copyAtlasToSpmDir.m
+26 −0 tests/test_copyAtlasToSpmDir.m
10 changes: 5 additions & 5 deletions src/defaults/checkOptions.m
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Expand Up @@ -204,12 +204,12 @@

% validate content of opt.results

defaultContrast = defaultResultsStructure();
defaultResults = defaultResultsStructure();

fields = fieldnames(defaultContrast);
fields = fieldnames(defaultResults);

if ~isfield(opt, 'results')
opt.results = defaultContrast;
opt.results = defaultResults;
return
end

Expand All @@ -226,12 +226,12 @@
end

% add missing fields
thisResult = setFields(thisResult, defaultContrast);
thisResult = setFields(thisResult, defaultResults);

% fill in empty fields
for i = 1:numel(fields)
if isempty(thisResult.(fields{i}))
thisResult.(fields{i}) = defaultContrast.(fields{i});
thisResult.(fields{i}) = defaultResults.(fields{i});
end
end

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27 changes: 14 additions & 13 deletions src/defaults/defaultResultsStructure.m
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Original file line number Diff line number Diff line change
@@ -1,24 +1,25 @@
function contrast = defaultResultsStructure()
function result = defaultResultsStructure()
%
% (C) Copyright 2019 CPP_SPM developers

contrast = defaultContrastsStructure;
result = defaultContrastsStructure;

contrast.png = true();
result.png = true();

contrast.csv = true();
result.csv = true();
result.atlas = 'Neuromorphometrics';

contrast.threshSpm = false();
result.threshSpm = false();

contrast.binary = false();
result.binary = false();

contrast.montage = struct('do', false(), ...
'slices', [], ...
'orientation', 'axial', ...
'background', fullfile(spm('dir'), ...
'canonical', ...
'avg152T1.nii'));
result.montage = struct('do', false(), ...
'slices', [], ...
'orientation', 'axial', ...
'background', fullfile(spm('dir'), ...
'canonical', ...
'avg152T1.nii'));

contrast.nidm = true();
result.nidm = true();

end
33 changes: 25 additions & 8 deletions src/utils/labelActivations.m
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Original file line number Diff line number Diff line change
@@ -1,13 +1,19 @@
function tsvFile = labelActivations(varargin)
%
% Adds MNI labels to a csv output file from SPM
% Adds MNI labels to a csv output file from SPM and saves it as SPM.
%
% Can choose which atlas to use.
%
% USAGE::
%
% tsvFile = labelActivations(csvFile)
% tsvFile = labelActivations(csvFile, 'atlas', 'Neuromorphometrics')
%
% :param csvFile:
% :type csvFile: path
% :type csvFile: path
%
% :param atlas: Any of ``{'Neuromorphometrics', 'AAL'}``.
% Defaults to ``'Neuromorphometrics'``
% :type atlas: char
%
% :returns: - :tsvFile: (path)
%
Expand All @@ -18,10 +24,21 @@
args = inputParser;

addRequired(args, 'csvFile', @ischar);
addParameter(args, 'atlas', 'Neuromorphometrics', @ischar);

parse(args, varargin{:});

csvFile = args.Results.csvFile;
atlas = args.Results.atlas;

atlasName = 'Neuromorphometrics';
if ~strcmp(atlas, 'Neuromorphometrics')
copyAtlasToSpmDir(atlas, 'verbose', false);
switch atlas
case 'AAL'
atlasName = 'AAL3v1_1mm';
end
end

%% renaming headers to have only one row
% combine 1rst and 2nd row
Expand Down Expand Up @@ -61,13 +78,13 @@
end

%% add MNI label
% L = spm_atlas('list');
xA = spm_atlas('load', 'Neuromorphometrics');
spm_atlas('list', 'installed', '-refresh');
xA = spm_atlas('load', atlasName);

for i = 1:numel(newCSV.x)
newCSV.neuromorphometric_label{i} = spm_atlas('query', xA, [newCSV.x(i), ...
newCSV.y(i), ...
newCSV.z(i)]');
newCSV.([atlas '_label']){i} = spm_atlas('query', xA, [newCSV.x(i), ...
newCSV.y(i), ...
newCSV.z(i)]');
end

tsvFile = bids.internal.file_utils(csvFile, 'ext', '.tsv');
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2 changes: 1 addition & 1 deletion src/workflows/stats/bidsResults.m
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Expand Up @@ -586,7 +586,7 @@ function renameOutputResults(results)

for iFile = 1:size(csvFiles, 1)
source = deblank(csvFiles(iFile, :));
labelActivations(source);
labelActivations(source, 'atlas', result.atlas);
end

end
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2 changes: 1 addition & 1 deletion tests/dummyData/tsv_files/moae_results_table.tsv
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@@ -1,4 +1,4 @@
set_p set_c cluster_p_FWE_corr_ cluster_p_FDR_corr_ cluster_equivk cluster_p_unc_ peak_p_FWE_corr_ peak_p_FDR_corr_ peak_T peak_equivZ peak_p_unc_ x y z neuromorphometric_label
set_p set_c cluster_p_FWE_corr_ cluster_p_FDR_corr_ cluster_equivk cluster_p_unc_ peak_p_FWE_corr_ peak_p_FDR_corr_ peak_T peak_equivZ peak_p_unc_ x y z Neuromorphometrics_label
0.000 4 0.000 0.000 218 0.000 0.000 0.000 12.15 Inf 0.000 57 -22 11 Right PT planum temporale
n/a n/a n/a n/a n/a n/a 0.000 0.000 11.38 Inf 0.000 66 -13 -4 Right STG superior temporal gyrus
n/a n/a n/a n/a n/a n/a 0.000 0.003 7.02 6.05 0.000 60 -37 5 Right MTG middle temporal gyrus
Expand Down
9 changes: 9 additions & 0 deletions tests/dummyData/tsv_files/moae_results_table_aal.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
set_p set_c cluster_p_FWE_corr_ cluster_p_FDR_corr_ cluster_equivk cluster_p_unc_ peak_p_FWE_corr_ peak_p_FDR_corr_ peak_T peak_equivZ peak_p_unc_ x y z AAL_label
0.000 4 0.000 0.000 218 0.000 0.000 0.000 12.15 Inf 0.000 57 -22 11 Temporal_Sup_R
n/a n/a n/a n/a n/a n/a 0.000 0.000 11.38 Inf 0.000 66 -13 -4 Temporal_Sup_R
n/a n/a n/a n/a n/a n/a 0.000 0.003 7.02 6.05 0.000 60 -37 5 Temporal_Mid_R
n/a n/a 0.000 0.000 401 0.000 0.000 0.000 12.11 Inf 0.000 -63 -28 11 Temporal_Sup_L
n/a n/a n/a n/a n/a n/a 0.000 0.000 11.31 Inf 0.000 -45 -34 11 Temporal_Sup_L
n/a n/a n/a n/a n/a n/a 0.000 0.000 10.10 7.84 0.000 -66 -10 -1 Temporal_Mid_L
n/a n/a 0.001 0.016 5 0.012 0.005 0.161 5.86 5.24 0.000 69 -25 -4 Temporal_Mid_R
n/a n/a 0.015 0.219 1 0.219 0.032 0.684 5.40 4.90 0.000 51 5 -7 Insula_R
9 changes: 9 additions & 0 deletions tests/dummyData/tsv_files/moae_results_table_neuromorpho.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
set_p set_c cluster_p_FWE_corr_ cluster_p_FDR_corr_ cluster_equivk cluster_p_unc_ peak_p_FWE_corr_ peak_p_FDR_corr_ peak_T peak_equivZ peak_p_unc_ x y z Neuromorphometrics_label
0.000 4 0.000 0.000 218 0.000 0.000 0.000 12.15 Inf 0.000 57 -22 11 Right PT planum temporale
n/a n/a n/a n/a n/a n/a 0.000 0.000 11.38 Inf 0.000 66 -13 -4 Right STG superior temporal gyrus
n/a n/a n/a n/a n/a n/a 0.000 0.003 7.02 6.05 0.000 60 -37 5 Right MTG middle temporal gyrus
n/a n/a 0.000 0.000 401 0.000 0.000 0.000 12.11 Inf 0.000 -63 -28 11 Left PT planum temporale
n/a n/a n/a n/a n/a n/a 0.000 0.000 11.31 Inf 0.000 -45 -34 11 Left PT planum temporale
n/a n/a n/a n/a n/a n/a 0.000 0.000 10.10 7.84 0.000 -66 -10 -1 Left STG superior temporal gyrus
n/a n/a 0.001 0.016 5 0.012 0.005 0.161 5.86 5.24 0.000 69 -25 -4 Right MTG middle temporal gyrus
n/a n/a 0.015 0.219 1 0.219 0.032 0.684 5.40 4.90 0.000 51 5 -7 Right PP planum polare
1 change: 1 addition & 0 deletions tests/tests_defaults/test_defaultResultsStructure.m
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Expand Up @@ -24,6 +24,7 @@ function test_defaultResultsStructure_basic()
expected.png = true();

expected.csv = true();
expected.atlas = 'Neuromorphometrics';

expected.threshSpm = false();

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23 changes: 22 additions & 1 deletion tests/tests_unit/test_labelActivations.m
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Expand Up @@ -7,6 +7,27 @@
initTestSuite;
end

function test_labelActivations_aal()

if isGithubCi()
return
end

csvFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table.csv');

tsvFile = labelActivations(csvFile, 'atlas', 'AAL');

assertEqual(exist(tsvFile, 'file'), 2);

expectedFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table_aal.tsv');
expectedContent = bids.util.tsvread(expectedFile);

content = bids.util.tsvread(tsvFile);

assertEqual(content, expectedContent);

end

function test_labelActivations_basic()

csvFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table.csv');
Expand All @@ -15,7 +36,7 @@ function test_labelActivations_basic()

assertEqual(exist(tsvFile, 'file'), 2);

expectedFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table.tsv');
expectedFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table_neuromorpho.tsv');
expectedContent = bids.util.tsvread(expectedFile);

content = bids.util.tsvread(tsvFile);
Expand Down