Hi everyone,
I am hoping someone can clarify what some of the optional flags in fsl_regfilt are doing.
Specifically
-F -freqfilt
-freq_ic_smooth
I am likely grossly misunderstanding but does this mean that fsl_regfilt, much like AFNI’s 3dTproject can do frequency filtering (-passband) and confound regression in one step, with the added option of smoothing the data?
If so, can someone clarify how to appropriately use these flags? For instance, is the --fthresh (frequency threshold ratio - default: 0.15) and --fthresh2 (frequency filter score threshold - default: 0.02) performing a bandpass filter between 0.02 and 0.15 Hz? Also, is the -freq_ic_smooth input meant to me a sigma or a FWHM mm value?
Thank you in advance, the fsl_regfilt options are listed below
fsl_regfilt
Part of FSL (ID: 6.0.1)
fsl_regfilt
Author: Christian F. Beckmann
Copyright© 2016-2013 University of Oxford
Data de-noising by regressing out part of a design matrix
using simple OLS regression on 4D images
Usage:
fsl_regfilt -i -d -f -o [options]
Compulsory arguments (You MUST set one or more of):
-i,–in input file name (4D image)
-o,–out output file name for the filtered data
-d,–design file name of the matrix with time courses (e.g. GLM design or MELODIC mixing matrix)
Optional arguments (You may optionally specify one or more of):
-m,–mask mask image file name
-f,–filter filter out part of the regression model, e.g. -f “1,2,3”
-F,–freqfilt filter out components based on high vs. low frequency content
–freq_ic switch off IC Z-stats filtering as part of frequency filtering
–freq_ic_smooth smoothing width for IC Z-stats filtering as part of frequency filtering
–fthresh frequency threshold ratio - default: 0.15
–fthresh2 frequency filter score threshold - default: 0.02
–vn perform variance-normalisation on data
-v switch on diagnostic messages
-a switch on aggressive filtering (full instead of partial regression)
-h,–help display this help text
–out_data output file name for pre-processed data (prior to denoising)
–out_mix output file name for new mixing matrix
–out_vnscales output file name for scaling factors from variance normalisation