Merge pull request #622 from cpp-lln-lab/olf

[ENH] add neuromorphometrics label to bidsResults output when in MNI space

Author: Remi-Gau

src/utils/labelActivations.m

@@ -0,0 +1,69 @@
+function tsvFile = labelActivations(varargin)
+  %
+  % Adds MNI labels to a csv output file from SPM
+  %
+  % USAGE::
+  %
+  %   tsvFile = labelActivations(csvFile)
+  %
+  % :param csvFile:
+  % :type csvFile: path
+  %
+  % :returns: - :tsvFile: (path)
+  %
+  % (C) Copyright 2022 CPP_SPM developers
+
+  % The code goes below
+
+  args = inputParser;
+
+  addRequired(args, 'csvFile', @ischar);
+
+  parse(args, varargin{:});
+
+  csvFile = args.Results.csvFile;
+
+  %% renaming headers to have only one row
+  % combine 1rst and 2nd row
+  CSV = bids.util.tsvread(csvFile);
+
+  headers = fieldnames(CSV);
+
+  columnIdx = @(x) find(~cellfun('isempty', regexp(headers, ['^' x '.*'], 'match')));
+  coerce = @(x) regexprep(x, '[^a-zA-Z0-9_]', '_');
+
+  set = columnIdx('set');
+  for i = 1:numel(set)
+    newCSV.(['set_' coerce(CSV.(headers{set(i)}){1})]) = CSV.(headers{set(i)})(2:end);
+  end
+
+  cluster = columnIdx('cluster');
+  for i = 1:numel(cluster)
+    newCSV.(['cluster_' coerce(CSV.(headers{cluster(i)}){1})]) = CSV.(headers{cluster(i)})(2:end);
+  end
+
+  peak = columnIdx('peak');
+  for i = 1:numel(peak)
+    newCSV.(['peak_' coerce(CSV.(headers{peak(i)}){1})]) = CSV.(headers{peak(i)})(2:end);
+  end
+
+  coordinates = columnIdx('x');
+  label = {'x', 'y', 'z'};
+  for i = 1:numel(coordinates)
+    newCSV.(label{i}) = str2double(CSV.(headers{coordinates(i)})(2:end));
+  end
+
+  %% add MNI label
+  %   L = spm_atlas('list');
+  xA = spm_atlas('load', 'Neuromorphometrics');
+
+  for  i = 1:numel(newCSV.x)
+    newCSV.neuromorphometric_label{i} = spm_atlas('query', xA, [newCSV.x(i), ...
+                                                                newCSV.y(i), ...
+                                                                newCSV.z(i)]');
+  end
+
+  tsvFile = bids.internal.file_utils(csvFile, 'ext', '.tsv');
+  bids.util.tsvwrite(tsvFile, newCSV);
+
+end

src/workflows/stats/bidsResults.m

@@ -481,8 +481,12 @@
 end
 
 function renameOutputResults(results)
+  %
   % we create new name for the nifti output by removing the
   % spmT_XXXX prefix and using the XXXX as label- for the file
+  %
+  % also rename PNG and labels activations
+  %
 
   for i = 1:numel(results)
 
@@ -510,13 +514,24 @@ function renameOutputResults(results)
 
     renamePng(result.dir);
 
+    if result.csv && isMni(result.space)
+
+      csvFiles = spm_select('FPList', result.dir, '^spm_.*[0-9].csv$');
+
+      for iFile = 1:size(csvFiles, 1)
+        source = deblank(csvFiles(iFile, :));
+        labelActivations(source);
+      end
+
+    end
+
   end
 
 end
 
 function renameNidm(opt, result, subLabel)
   %
-  % removes the _XXX suffix before the PNG extension.
+  % removes the _XXX suffix before the nidm extension.
 
   nidmFiles = spm_select('FPList', result.dir, '^spm_[0-9]{4}.nidm.zip$');
 

tests/dummyData/tsv_files/moae_results_table.csv

@@ -0,0 +1,10 @@
+set,set,cluster,cluster,cluster,cluster,peak,peak,peak,peak,peak,,,
+p,c,p(FWE-corr),p(FDR-corr),equivk,p(unc),p(FWE-corr),p(FDR-corr),T,equivZ,p(unc),x,y,z {mm}
+0.000,4,0.000,0.000,218,0.000,0.000,0.000, 12.15,  Inf,0.000, 57,-22, 11
+,,,,,,0.000,0.000, 11.38,  Inf,0.000, 66,-13, -4
+,,,,,,0.000,0.003,  7.02, 6.05,0.000, 60,-37,  5
+,,0.000,0.000,401,0.000,0.000,0.000, 12.11,  Inf,0.000,-63,-28, 11
+,,,,,,0.000,0.000, 11.31,  Inf,0.000,-45,-34, 11
+,,,,,,0.000,0.000, 10.10, 7.84,0.000,-66,-10, -1
+,,0.001,0.016,5,0.012,0.005,0.161,  5.86, 5.24,0.000, 69,-25, -4
+,,0.015,0.219,1,0.219,0.032,0.684,  5.40, 4.90,0.000, 51,  5, -7

tests/dummyData/tsv_files/moae_results_table.tsv

@@ -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	neuromorphometric_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

tests/tests_unit/test_labelActivations.m

@@ -0,0 +1,25 @@
+function test_suite = test_labelActivations %#ok<*STOUT>
+  % (C) Copyright 2022 CPP_SPM 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
+  end
+  initTestSuite;
+end
+
+function test_labelActivations_basic()
+
+  csvFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table.csv');
+
+  tsvFile = labelActivations(csvFile);
+
+  assertEqual(exist(tsvFile, 'file'), 2);
+
+  expectedFile = fullfile(getDummyDataDir(), 'tsv_files', 'moae_results_table.tsv');
+  expectedContent = bids.util.tsvread(expectedFile);
+
+  content = bids.util.tsvread(tsvFile);
+
+  assertEqual(content, expectedContent);
+
+end