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Script: Coherence tutorial, use CAT12-segmented MRI if present
1 parent 7e7a88e commit b212461

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Lines changed: 37 additions & 21 deletions

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‎doc/license.html‎

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@@ -5,7 +5,7 @@
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<body alink="#fff000" link="#fff000" vlink="#fff000">
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<h4><span style="font-family: Arial Black; color: #ffffff;"><strong>THERE IS NO UNDO BUTTON!<BR>SET UP A <FONT color=red>BACKUP</FONT> OF YOUR DATABASE</strong></span></h4>
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<HR>
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<!-- LICENCE_START -->Version: 3.251024 (24-Oct-2025)<br>
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<!-- LICENCE_START -->Version: 3.251029 (29-Oct-2025)<br>
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<span style="font-style: italic;">COPYRIGHT &copy; 2000-2025
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USC &amp; McGill University.<br>
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</span>

‎doc/updates.txt‎

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October 2025
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--------------------------------------------------------------
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September 2025
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- Anatomy: Option to export fiducal locations alongside MRI file
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- Anatomy: Option to align Surface to MRI, by setting fiducials in surface

‎toolbox/script/test_tutorial.m‎

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@@ -127,8 +127,9 @@ function test_tutorial(tutorialNames, dataDir, reportDir, bstUser, bstPwd)
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tutorial_connectivity();
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case 'tutorial_coherence'
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dataFile = bst_fullfile(dataDir, 'SubjectCMC.zip');
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dataFile = get_tutorial_data(dataDir, 'SubjectCMC.zip', bstUser, bstPwd);
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if ~exist(dataFile, 'file')
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dataFile = bst_fullfile(dataDir, 'SubjectCMC.zip');
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bst_websave(dataFile, 'https://download.fieldtriptoolbox.org/tutorial/SubjectCMC.zip');
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end
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if exist(dataFile, 'file')

‎toolbox/script/tutorial_coherence.m‎

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@@ -51,10 +51,12 @@ function tutorial_coherence(tutorial_dir, reports_dir)
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% Build the path of the files to import
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MriFilePath = fullfile(tutorial_dir, 'SubjectCMC', 'SubjectCMC.mri');
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MegFilePath = fullfile(tutorial_dir, 'SubjectCMC', 'SubjectCMC.ds');
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MriCat12Path = fullfile(tutorial_dir, 'SubjectCMC', 'cat12');
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% Check if the folder contains the required files
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if ~file_exist(MriFilePath) || ~file_exist(MegFilePath)
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error(['The folder ' tutorial_dir ' does not contain the folder from the file SubjectCMC.zip.']);
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end
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isMriSegmented = file_exist(bst_fullfile(MriCat12Path, 'SubjectCMC.nii.gz'));
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%% ===== CREATE PROTOCOL =====
@@ -75,16 +77,24 @@ function tutorial_coherence(tutorial_dir, reports_dir)
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%% ===== IMPORT ANATOMY =====
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% Process: Import MRI
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bst_process('CallProcess', 'process_import_mri', [], [], ...
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'subjectname', SubjectName, ...
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'mrifile', {MriFilePath, 'ALL'}, ...
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'nas', [0, 0, 0], ...
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'lpa', [0, 0, 0], ...
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'rpa', [0, 0, 0], ...
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'ac', [0, 0, 0], ...
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'pc', [0, 0, 0], ...
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'ih', [0, 0, 0]);
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if ~isMriSegmented
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% Process: Import MRI
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bst_process('CallProcess', 'process_import_mri', [], [], ...
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'subjectname', SubjectName, ...
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'mrifile', {MriFilePath, 'ALL'}, ...
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'nas', [ 84, 229, 143], ...
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'lpa', [ 9, 116, 102], ...
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'rpa', [155, 114, 101]);
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else
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% Process: Import anatomy folder
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bst_process('CallProcess', 'process_import_anatomy', [], [], ...
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'subjectname', SubjectName, ...
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'mrifile', {MriCat12Path, 'CAT12'}, ...
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'nvertices', 15000, ...
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'nas', [ 84, 229, 143], ...
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'lpa', [ 9, 116, 102], ...
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'rpa', [155, 114, 101]);
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end
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% Process: Generate head surface
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bst_process('CallProcess', 'process_generate_head', [], [], ...
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'subjectname', SubjectName, ...
@@ -313,15 +323,17 @@ function tutorial_coherence(tutorial_dir, reports_dir)
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%% ===== SOURCE ESTIMATION =====
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% Process: Segment MRI with CAT12
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bst_process('CallProcess', 'process_segment_cat12', [], [], ...
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'subjectname', SubjectName, ...
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'nvertices', 15000, ...
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'tpmnii', {'', 'Nifti1'}, ...
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'sphreg', 1, ...
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'vol', 1, ...
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'extramaps', 0, ...
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'cerebellum', 0);
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if ~isMriSegmented
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% Process: Segment MRI with CAT12
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bst_process('CallProcess', 'process_segment_cat12', [], [], ...
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'subjectname', SubjectName, ...
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'nvertices', 15000, ...
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'tpmnii', {'', 'Nifti1'}, ...
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'sphreg', 1, ...
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'vol', 1, ...
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'extramaps', 0, ...
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'cerebellum', 0);
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end
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% Process: Compute covariance (noise or data)
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bst_process('CallProcess', 'process_noisecov', sFileRawNotchHighAbs, [], ...
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'baseline', [18, 29], ...

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