Tissue-based nuisance regressors

The tmfc_physioreg function calculates tissue-based nuisance regressors. It is called automatically by the main function TMFC_denoise if the user has selected the corresponding options, or it can be run manually:

tmfc_physioreg(SPM_paths,subject_paths,func_paths,masks,options);

The outputs are saved in the TMFC_denoise/[WM*e*]_[CSF*e*]_[GM*d*] subfolders, where folder names encode the selected mask parameters (see Mask Generation):

  • WM*e* — probability threshold and number of erosion cycles.

  • CSF*e* — threshold and number of erosion cycles.

  • GM*d* — threshold and number of dilation cycles.

Generated files include (depending on user-selected options, see Denoising Options):

  • 2Phys.mat, 4Phys.mat, 8Phys.mat — WM/CSF signals.

  • GSR.mat, 2GSR.mat, 4GSR.mat — whole-brain signals.

  • [aCompCor_*WM_*CSF_Ort].mat — a fixed number of WM and CSF principal components (PCs). These files also include information on the variance explained by WM/CSF PCs per session and the mean variance explained across sessions.

  • [aCompCor50_Ort].mat — a variable number of PCs explaining 50% of WM/CSF signals variance. This file also reports the mean and total number of PCs for WM and CSF across sessions.

Note: When pre-orthogonalization of WM and CSF signals is enabled before PC extraction, the suffix _Ort is appended to all aCompCor output files.