Command Line Usage

All functions in TMFC_denoise can be executed directly from the MATLAB command line or used in custom scripts without the GUI.

Example scripts demonstrating typical command-line usage are available in the examples folder of the TMFC_denoise GitHub repository:

• prepare_auditory_dataset.m — prepares the auditory fMRI dataset from the SPM website: http://www.fil.ion.ucl.ac.uk/spm/data/auditory/

• prepare_facerep_dataset.m — prepares the face repetition fMRI dataset from the SPM website: http://www.fil.ion.ucl.ac.uk/spm/data/face_rep/

• TMFC_denoise_Example_01_Auditory_dataset.m — example of TMFC_denoise usage (block design, auditory dataset).

• TMFC_denoise_Example_02_Facerep_dataset.m — example of TMFC_denoise usage (event-related design, face repetition dataset).

These scripts illustrate the full processing workflow, including dataset preparation, mask generation, denoising, and quality-control steps. They can be used as templates for adapting TMFC_denoise to other fMRI studies.