Prepare Your Data

TMFC_denoise uses information from SPM.mat files to obtain paths to functional images and SPM binary masks.

Original GLMs

The original model must be estimated (not only specified) in SPM12 or SPM25.

Note: Original models must include six head motion regressors, and the specified functinal images must be realigned and normalized (smoothing is optional).

If you estimated first-level GLMs and later moved the GLM or functinal-image folders to another location, you need to update the paths specified in the SPM.mat files (SPM.xY.VY and SPM.swd fields).

To change paths in SPM.mat files using the GUI, enter the following command in the MATLAB window:

tmfc_change_paths_GUI

If you use the TMFC toolbox GUI, click Tools → Change paths.

Select the subjects whose SPM.mat files you want to update. Enter the old path pattern (see SPM.swd field in the SPM.mat file) and the new path pattern:

Change paths GUI.

To change paths in SPM.mat files from the command line, enter:

tmfc_change_paths_GUI(SPM_paths, old_path, new_path)

Structural Images

To calculate tissue-based regressors and/or DVARS, you need to create tissue-specific binary masks. These masks are generated from unprocessed T1-weighted structural images. Structural images must be in native space, since binary masks are created in native space and later normalized to MNI space.

Structural images can be coregistered with functional images (optional). This is not necessary because TMFC_denoise automatically coregisters the skull-stripped structural image and binary masks to the functional images.

Structural images may be in *.img/*.hdr, *.nii, or *.nii.gz format.

Note: To automatically select structural images using the GUI, they must: - Have the same root folder and subfolder structure, - Share the same file format, and - Have a consistent name pattern (to be uniquely detected via a text filter, e.g., *T1*.nii*).

Functional Images

To calculate tissue-based regressors or DVARS, you should extract tissue-specific signals from unsmoothed functional images. Functional images must be realigned and normalized, as binary masks are normalized to MNI space.

If your original model was specified for unsmoothed images, simply press Preserve functional image paths from the SPM.mat files during functional image selection. If your model was specified for smoothed images, you need to provide paths to unsmoothed images.

In principle, tissue-specific signals can be extracted from smoothed images (e.g., if unsmoothed data are unavailable), but unsmoothed images are preferred for noise-regressor creation.

Images can be either *.img/*.hdr (3D) or *.nii (3D/4D). The *.nii.gz format is not supported.

Note: To automatically select functional images using the GUI, they must: - Have the same root folder and subfolder structure, - Share the same file format, and - Follow a consistent name pattern (to be uniquely detected via a text filter, e.g., *war*.nii).