[FIX] remove dummies from preproc and not raw when using cli (#1057)

* remove dummies from preproc when using cli

* update changelog

* octave fix

* fix link

Author: Remi-Gau

CHANGELOG.md

@@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-<!-- **Full Changelog**: https://github.com/cpp-lln-lab/CPP_SPM/compare/v3.0.0...v3.1.0 -->
+<!-- **Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v3.0.0...v3.1.0 -->
 
 ### Added
 
@@ -57,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [FIX] remove dummies from preproc dataset and not raw dataset when using CLI (#1057) @Remi-Gau
 * [FIX] skip smoothing when running bidspm prepoc in dryRun (#1054) @Remi-Gau
 * [FIX] handle phase entity in filename (#1034) @Remi-Gau
 * [FIX] fix group level results after contrasts smoothing  (#1021) @Remi-Gau
@@ -75,7 +76,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [3.0.0] - 2022-12-14
 
-**Full Changelog**: https://github.com/cpp-lln-lab/CPP_SPM/compare/v2.3.0...v3.0.0
+**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v2.3.0...v3.0.0
 
 ### Changed
 
@@ -106,7 +107,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [2.3.0] - 2022-11-22
 
-**Full Changelog**: https://github.com/cpp-lln-lab/CPP_SPM/compare/v2.2.0...v2.3.0
+**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v2.2.0...v2.3.0
 
 - `bidspm` main function:
   - saving options are saved to help with bug report
@@ -141,7 +142,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [2.2.0] - 2022-10-29
 
-**Full Changelog**: https://github.com/cpp-lln-lab/CPP_SPM/compare/v2.1.0...v2.2.0
+**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v2.1.0...v2.2.0
 
 ### Added
 
@@ -164,7 +165,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [2.1.0] - 2022-07-21
 
-**Full Changelog**: https://github.com/cpp-lln-lab/CPP_SPM/compare/v2.0.0...v2.0.1
+**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v2.0.0...v2.0.1
 
 ### Added
 
@@ -213,7 +214,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [2.0.0] - 2022-07-10
 
-**Full Changelog**: https://github.com/cpp-lln-lab/CPP_SPM/compare/v1.1.5...v2.0.0
+**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v1.1.5...v2.0.0
 
 ### Added
 

bidspm.m

@@ -274,8 +274,10 @@ function preprocess(args)
   end
   bidsCopyInputFolder(opt);
   if opt.dummy_scans > 0
-    bidsRemoveDummies(opt, ...
-                      'dummyScans', opt.dummy_scans, ...
+    tmpOpt = opt;
+    tmpOpt.dir.input = tmpOpt.dir.preproc;
+    bidsRemoveDummies(tmpOpt, ...
+                      'dummyScans', tmpOpt.dummy_scans, ...
                       'force', false);
   end
   bidsCheckVoxelSize(opt);

src/workflows/preproc/bidsRemoveDummies.m

@@ -6,18 +6,17 @@ function bidsRemoveDummies(varargin)
   %
   %  bidsRemoveDummies(opt, 'dummyScans', someInteger, 'force', false)
   %
-  % :type opt:  structure
   % :param opt: Options chosen for the analysis.
   %             See also: checkOptions
   %             ``checkOptions()`` and ``loadAndCheckOptions()``.
   % :type opt: structure
   %
   % :param dummyScans: number of volumes to remove
-  % :type dummyScans: integer >= 0
+  % :type  dummyScans: integer >= 0
   %
   % :param force: use ``'force', true`` to remove dummy scans even if metadata say
   %               they have already been removed
-  % :type force: boolean
+  % :type  force: boolean
   %
   % EXAMPLE::
   %
@@ -69,6 +68,7 @@ function bidsRemoveDummies(varargin)
 
     filter = opt.bidsFilterFile.bold;
     filter.ext = '\.nii.*$';
+    filter.prefix = '';
     filter.task = opt.taskName;
     filter.desc = '';
     filter.space = '';

tests/tests_workflows/preproc/test_bidsRemoveDummies.m

@@ -10,7 +10,20 @@
 
 function test_bidsRemoveDummies_basic()
 
+  if bids.internal.is_octave()
+    tmpDir = fullfile(tempname);
+  else
+    tmpDir = fullfile(tempname, 'raw');
+  end
+  spm_mkdir(tmpDir);
   opt = setOptions('MoAE');
-  bidsRemoveDummies(opt, 'dummyScans', 12, 'force', false);
+  copyfile(opt.dir.raw, tmpDir);
+
+  if bids.internal.is_octave()
+    tmpDir = fullfile(tmpDir, 'raw');
+  end
+  opt.dir.raw = tmpDir;
+  opt.dir.input = tmpDir;
+  bidsRemoveDummies(opt, 'dummyScans', 20, 'force', false);
 
 end