Merge pull request #418 from Remi-Gau/bug-fix

[FIX] remove extra submodules and properly compute run level contrasts

Author: Remi-Gau

.github/workflows/run_system_tests.yml

@@ -17,14 +17,12 @@ name: system tests
 on:
   push:
     branches:
-      - master
       - main
   pull_request:
     branches: 
-      - 'master'
       - 'main'
   schedule:
-    - cron: "* * 1 * *"
+    - cron: "0 0 1 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent

.github/workflows/run_tests.yml

@@ -21,7 +21,7 @@ on:
   pull_request:
     branches: '*'
   schedule:
-    - cron: "* * 1 * *"
+    - cron: "0 0 1 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent

.gitmodules

@@ -12,4 +12,4 @@
 	url = https://github.com/bramzandbelt/slice_display.git
 [submodule "lib/brain_colours"]
 	path = lib/brain_colours
-	url = https://github.com/CPernet/brain_colours.git
+	url = https://github.com/CPernet/brain_colours.git

demos/MoAE/moae_create_roi_extract_data.m

@@ -23,7 +23,7 @@
 % we get the con image to extract data
 % we can do this by using the "label-XXXX" from the mask
 p = bids.internal.parse_filename(spm_file(maskImage, 'filename'));
-conImage = spm_select('FPList', ffxDir, ['^con_' p.label '.nii$']);
+conImage = spm_select('FPList', ffxDir, ['^con_' p.entities.label '.nii$']);
 
 %% Create ROI right auditory cortex
 sphere.location = [57 -22 11];
@@ -35,12 +35,12 @@
 [~, roiFile] = createRoi('expand', specification, conImage, pwd, saveROI);
 
 % rename mask image
-newname.desc = 'right auditory cortex';
-newname.task = '';
-newname.label = '';
-newname.p = '';
-newname.k = '';
-newname.MC = '';
+newname.entities.desc = 'right auditory cortex';
+newname.entities.task = '';
+newname.entities.label = '';
+newname.entities.p = '';
+newname.entities.k = '';
+newname.entities.MC = '';
 rightRoiFile = renameFile(roiFile, newname);
 
 %% same but with left hemisphere

demos/MoAE/moae_run.m

@@ -23,7 +23,7 @@
 download_moae_ds(downloadData);
 
 %% Run batches
-reportBIDS(opt);
+% reportBIDS(opt);
 bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping

demos/MoAE/moae_slice_display.m

@@ -31,7 +31,7 @@
 %
 %   - t-statistics opacity-coded
 
-spmTImage = spm_select('FPList', ffxDir, ['^spmT_' p.label '.nii$']);
+spmTImage = spm_select('FPList', ffxDir, ['^spmT_' p.entities.label '.nii$']);
 layers(2).opacity.file = spmTImage;
 
 layers(2).opacity.range = [2 3];

lib/CPP_ROI

@@ -47,7 +47,7 @@
 
   %% Run batches
 
-  reportBIDS(opt);
+  % reportBIDS(opt);
 
   bidsCopyRawFolder(opt, 1);
 

lib/bids-matlab

@@ -59,7 +59,7 @@
   matlabbatch{end}.spm.stats.fmri_est.spmmat = spmMatFile;
 
   writeResiduals = true();
-  if ~opt.glm.QA.do
+  if ~opt.QA.glm.do
     writeResiduals = false();
   end
   matlabbatch{end}.spm.stats.fmri_est.write_residuals = writeResiduals;