From bea0640871a408cbf2a1e83129bd5c4d373b04ed Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 13 Jul 2024 18:49:52 +0200
Subject: [PATCH] [FIX] run test create roi octave (#1285)

* run test create roi octave

* fix several tests in cpp roi

* reset submod

* update CPP_ROI

* fix default path output create roi

* fix typo
---
 lib/CPP_ROI                                   |  2 +-
 src/bidspm/bidspm.py                          |  2 +-
 src/workflows/roi/bidsCreateROI.m             |  2 +-
 .../tests_cli/test_bidspm_create_roi.m        | 26 +++++--------------
 4 files changed, 9 insertions(+), 23 deletions(-)

diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index 4b4f7f2b5..b3cd28214 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit 4b4f7f2b5614fc2b30d807a2e05b73baa2a34c0f
+Subproject commit b3cd28214430e33dc4f3c1ad32a1ba325a711a9c
diff --git a/src/bidspm/bidspm.py b/src/bidspm/bidspm.py
index 62fd4e6f2..d591db9ce 100755
--- a/src/bidspm/bidspm.py
+++ b/src/bidspm/bidspm.py
@@ -186,7 +186,7 @@ def create_roi(
 ) -> str:
     roi_name = "{ '" + "', '".join(roi_name) + "' }" if roi_name is not None else None  # type: ignore
     if roi_dir is None:
-        roi_dir = Path()
+        roi_dir = output_dir
 
     cmd = generate_cmd(
         bids_dir=bids_dir,
diff --git a/src/workflows/roi/bidsCreateROI.m b/src/workflows/roi/bidsCreateROI.m
index 6ba1bf998..f7cb9f0a9 100644
--- a/src/workflows/roi/bidsCreateROI.m
+++ b/src/workflows/roi/bidsCreateROI.m
@@ -14,7 +14,7 @@ function bidsCreateROI(opt)
   %   opt.roi.atlas = 'wang';
   %   opt.roi.hemi = {'L', 'R'};
   %   opt.roi.name = {'V1v', 'V1d'};
-  %   opt.roi.space = {'IXI549Space''};
+  %   opt.roi.space = {'IXI549Space'};
   %
   %   bidsCreateROI(opt);
   %
diff --git a/tests/tests_slow/tests_cli/test_bidspm_create_roi.m b/tests/tests_slow/tests_cli/test_bidspm_create_roi.m
index 039b41405..7bca3de11 100644
--- a/tests/tests_slow/tests_cli/test_bidspm_create_roi.m
+++ b/tests/tests_slow/tests_cli/test_bidspm_create_roi.m
@@ -13,10 +13,6 @@ function test_bidsCreateROI_boilerplate_only()
 
   markTestAs('slow');
 
-  if bids.internal.is_octave
-    moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
-  end
-
   outputPath = tempName();
 
   bidspm(pwd, outputPath, ...
@@ -40,10 +36,6 @@ function test_bidsCreateROI_glasser()
 
   markTestAs('slow');
 
-  if bids.internal.is_octave
-    moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
-  end
-
   outputPath = tempName();
 
   bidspm(pwd, outputPath, ...
@@ -54,6 +46,12 @@ function test_bidsCreateROI_glasser()
          'space', {'IXI549Space'}, ...
          'verbosity', 3);
 
+  assert(exist(fullfile(outputPath, ...
+                        'derivatives', ...
+                        'bidspm-roi', ...
+                        'reports', ...
+                        'create_roi_atlas-glasser_citation.md'), 'file') == 2);
+
   rois = spm_select('FPList', fullfile(outputPath, ...
                                        'derivatives', ...
                                        'bidspm-roi', 'group'), '.*glasser.*_mask\.nii');
@@ -65,10 +63,6 @@ function test_bidsCreateROI_wang()
 
   markTestAs('slow');
 
-  if bids.internal.is_octave
-    moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
-  end
-
   outputPath = tempName();
 
   bidspm(pwd, outputPath, ...
@@ -90,10 +84,6 @@ function test_bidsCreateROI_neuromorphometrics()
 
   markTestAs('slow');
 
-  if bids.internal.is_octave
-    moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
-  end
-
   outputPath = tempName();
 
   bidspm(pwd, outputPath, ...
@@ -133,10 +123,6 @@ function test_bidsCreateROI_one_hemisphere()
 
   markTestAs('slow');
 
-  if bids.internal.is_octave
-    moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
-  end
-
   outputPath = tempName();
 
   bidspm(pwd, outputPath, 'subject', ...