Installation

You can install TMFC_denoise either:

1. As a standalone toolbox, or

2. As part of the TMFC toolbox (https://github.com/IHB-IBR-department/TMFC_toolbox).

Dependencies

Before using TMFC_denoise, make sure the following software is installed:

• MATLAB R2021b or newer

• SPM12 or SPM25

• (Optional) Parallel Computing Toolbox – for parallel computations

Download

You can obtain the toolbox from any of the following sources:

• GitHub repository: https://github.com/IHB-IBR-department/TMFC_denoise

• Zenodo DOI: https://doi.org/10.5281/zenodo.17176264

• Included in the TMFC toolbox: https://github.com/IHB-IBR-department/TMFC_toolbox

Installation Steps

1. Download and unzip the toolbox archive from GitHub or Zenodo.

2. In MATLAB, open Home ‣ Set Path ‣ Add with Subfolders.

3. Select the TMFC_denoise folder (or the TMFC_toolbox folder, if using the integrated version).

4. Click Save and Close.

5. Test the installation:

   TMFC_denoise
   

   This command should open the TMFC_denoise GUI.

Alternatively, if you installed the full TMFC toolbox:

TMFC

Then, in the main TMFC GUI, choose Tools ‣ Denoise.

Command-Line Usage

The TMFC_denoise toolbox can also be executed without using the GUI:

output_paths = TMFC_denoise(SPM_paths,subject_paths,options)

output_paths = TMFC_denoise(SPM_paths,subject_paths,options,anat_paths,func_paths)

output_paths = TMFC_denoise(SPM_paths,subject_paths,options,anat_paths,func_paths,display_FD,estimate_GLMs,clear_all)

For command-line examples, see the examples folder in the GitHub repository: examples folder of the TMFC_denoise GitHub repository