HMP expansions and FD plots

The function tmfc_head_motion calculates HMP expansions and the FD time series. Also calculates task-FD correlations. It is called automatically by the main function TMFC_denoise or can be run manually:

FD = tmfc_head_motion(SPM_paths,subject_paths,options);

The outputs are saved in the TMFC_denoise subfolder within each subject’s first-level GLM directory: 12HMP.mat, 24HMP.mat, and FD.mat. The FD.mat file contains FD time series for each session, session-wise mean and maximum FD values, session-wise task-FD correlations, and mean/max FD across all sessions:

FD.mat file
Field	Description
SPM_path	Full path to original SPM.mat file.
Subject	Subject folder name.
Sess (struct)	Session-wise FD data: FD_ts: FD time-series per session FD_mean: Mean FD per session FD_max: Max FD per session taskFD_corr_mean: Mean task-FD correlation per session taskFD_corr_maxabs: Maximum abs(task-FD correlation) per session taskFD_corr_maxabs_name: Name of the corresponding task condition
FD_mean	Mean FD across all sessions.
FD_max	Max FD across all sessions.
taskFD_corr_mean	Mean task-FD correlation across all sessions.
taskFD_corr_maxabs	Maximum abs(task-FD correlation) across all sessions.
taskFD_corr_maxabs_name	Name of the corresponding task condition.

Framewise Displacement Plot

The GUI window for FD time-series inspection is opened with tmfc_plot_FD. It is called automatically by the main function TMFC_denoise. This interface allows users to change the FD threshold using the Set FD threshold [mm] button and to calculate the number of flagged time points exceeding this threshold. The selected threshold is subsequently applied during spike regression, if that denoising option is chosen.

To open FD plot GUI manually run:

% Allows saving group FD statistics only:
FDthr = tmfc_plot_FD(FD);

% Allows saving group FD statistics and TMFC denoise settings:
FDthr = tmfc_plot_FD(FD,options,SPM_paths,subject_paths,anat_paths,func_paths);

Pressing the Save button stores individual subject FD data and group-wise FD statistics in a single *.mat file:

Group_FD.mat file
Field	Description
denoising_settings (struct)	Selected TMFC_denoise settings: SPM_paths: see Select Subjects subject_paths: see Select Subjects options: see Denoising Options anat_paths: see Select Structural Images func_paths: see Select Functional Images
FD (struct)	Individual FD data for all subjects (see FD.mat table).
FDthr	FD threshold (in millimeters).
flagged (struct)	Flagged time points for each subject. Sess: Number of flagged time points per session total: Total number of flagged time points total_prc: Percentage of flagged time points (total)
max_flagged	Maximum number of flagged time points across subjects.
mean_flagged	Mean number of flagged time points across subjects.
min_flagged	Minimum number of flagged time points across subjects.
N_25prc	Number of subjects with >25% of scans above the selected FD threshold.
N_50prc	Number of subjects with >50% of scans above the selected FD threshold.
N_75prc	Number of subjects with >75% of scans above the selected FD threshold.
N_95prc	Number of subjects with >95% of scans above the selected FD threshold.
sd_flagged	SD number of flagged time points across subjects.