[ENH] allow to copy anat only on raw datasets (#1181)

* allow to copy anat only on raw datasets

* update changelog

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+* [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
 * [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

src/IO/getData.m

@@ -97,7 +97,7 @@
   if isfield(opt, 'taskName') && ~any(ismember(opt.taskName, bids.query(BIDS, 'tasks')))
 
     msg = sprintf(['The task %s that you have asked for ', ...
-                   'does not exist in this data set.\n', ...
+                   'does not exist in this dataset.\n', ...
                    'List of tasks present in this dataset:\n%s'], ...
                   strjoin(opt.taskName), ...
                   bids.internal.create_unordered_list(bids.query(BIDS, 'tasks')));

src/cli/cliCopy.m

@@ -20,6 +20,12 @@ function cliCopy(varargin)
 
   opt.query.desc = {'preproc', 'brain'};
   opt.query.suffix = {'T1w', 'bold', 'mask'};
+  if opt.anatOnly
+    opt.query.suffix = {'T1w', 'mask'};
+  end
+  if isempty(opt.taskName)
+    opt = rmfield(opt, 'taskName');
+  end
   opt.query.space = opt.space;
 
   bidsFilterFile = getBidsFilterFile(args);

src/workflows/bidsCopyInputFolder.m

@@ -3,7 +3,7 @@ function bidsCopyInputFolder(varargin)
   % Copies data from the ``opt.dir.input`` folder to the ``opt.dir.output`` folder
   %
   % Then it will search the derivatives directory for any zipped ``*.gz`` image
-  % and uncompress the files for the task of interest.
+  % and uncompress the files of interest.
   %
   % USAGE::
   %
@@ -56,6 +56,21 @@ function bidsCopyInputFolder(varargin)
 
   [BIDS, opt] = getData(opt, opt.dir.input);
 
+  skip_derivative_entities = false;
+  if ~isfield(BIDS.description, 'DatasetType')  || ...
+      (isfield(BIDS.description, 'DatasetType') && ...
+       strcmp(BIDS.description.DatasetType, 'raw'))
+    skip_derivative_entities = true;
+  end
+  if skip_derivative_entities
+    entities_to_skip = {'hemi', 'space', 'seg', 'res', 'den', 'label', 'desc'};
+    for i = 1:numel(entities_to_skip)
+      if isfield(opt.query, entities_to_skip{i})
+        opt.query = rmfield(opt.query, entities_to_skip{i});
+      end
+    end
+  end
+
   for iModality = 1:numel(opt.query.modality)
 
     skip_dependencies = false;

tests/tests_cli/test_bidspm_copy_raw.m

@@ -0,0 +1,29 @@
+function test_suite = test_bidspm_copy_raw %#ok<*STOUT>
+
+  % (C) Copyright 2023 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
+  end
+  initTestSuite;
+end
+
+function test_copy_anat_only()
+
+  inputPath = fullfile(getMoaeDir(), 'inputs', 'raw');
+
+  outputPath = tempName();
+
+  bidspm(inputPath, outputPath, 'subject', ...
+         'action', 'copy', ...
+         'anat_only', true, ...
+         'verbosity', 0);
+
+  BIDS = bids.layout(fullfile(outputPath, 'derivatives', 'bidspm-preproc'), ...
+                     'verbose', false, ...
+                     'use_schema', false);
+
+  assertEqual(numel(bids.query(BIDS, 'data')), 1);
+
+end