GLM and related operations
glm_4dfp
multivariate voxelwise regression/correlation
Usage: glm_4dfp <format|fmtfile> <profile> <4dfp|conc input>
Examples:
glm_4dfp "4x124+" doubletask.txt b1_rmsp_dbnd_xr3d_norm
Options
-Z |
supress automatic removal of mean from input regressors |
-C<str> |
read partial beta coefficients from specified 4dfp image (default compute) |
-o[str] |
save partial beta images with specified trailer (default = “coeff”) |
-R |
compute partial beta images as percent modulation |
-b[str] |
save total beta images with specified trailer (default = “tbeta”) |
-p[str] |
save partial corr images with specified trailer (default = “pcorr”) |
-t[str] |
save total corr images with specified trailer (default = “tcorr”) |
-r[str] |
save residual timeseries with specified trailer (default = “resid”) |
-@<b|l> |
output big or little endian (default input endian) |
N.B.: conc files must have extension “conc” N.B.: <profile> lists temporal profiles (ASCII npts x ncol; ‘#’ introduces comments) N.B.: <profile> line limits are 81920 chars and 8192 fields N.B.: absent -C, options -o and -r require design matrix inversion; dimension limit 256
actmapf_4dfp
voxelwise evaluate timeseries inner product against reference waveform
Usage: actmapf_4dfp <format|fmtfile> <4dfp|conc input>
Examples:
actmapf_4dfp -zu "3x3(11+4x15-)" b1_rmsp_dbnd_xr3d_norm
actmapf_4dfp -aanatomy -c10 -u "+" ball_dbnd_xr3d.conc
actmapf_4dfp -zu "4x124+" b1_rmsp_dbnd_xr3d -wweights.txt
Options
-a<str> |
specify 4dfp output root trailer (default = “actmap”) |
-c<flt> |
scale output by specified factor |
-u |
scale weights to unit variance |
-z |
adjust weights to zero sum |
-R |
compute relative modulation (default absolute) |
-w<weight file> |
read (text) weights from specified filename |
-@<b|l> |
output big or little endian (default input endian) |
N.B.: conc files must have extension “conc” N.B.: when using weight files ‘x’ frames in format are not counted N.B.: relative modulation images are zeroed where mean intensity < 0.5*whole_image_mode
GC_4dfp
Granger causality mapping Usage: GC_4dfp <format> <4dfp|conc input> <order>
Examples:
GC_4dfp "4(4x190+)" VB20579_rmsp_faln_dbnd_xr3d_atl.conc 2
Options
-w<str> |
specify timecourse profile file (one or more columns) |
-i<int> |
use only specified column (counting from 1) of timecourse profile |
-a<str> |
append specifed string to map output |
-g |
write lagged covariance (gamma) 4dfp stack |
-D |
write difference of directed influences (Fx->y - Fy->x) map |
-Z |
write Geweke “N(0,2)” measure (difference of square roots) map |
-F |
write Fx,y, Fx->y, Fy->x, Fx.y map stack |
-@<b|l> |
output big or little endian (default input endian) |
N.B.: conc files must have extension “conc” N.B.: effective frame count is determined by <format> N.B.: ‘x’ frames in format are not counted
GC_dat
Granger causality on ASCII column data
Usage: GC_dat <format> <input_datafile> <order>
Examples:
GC_dat "4x106+" ROI_timeseries.dat 2
Options
-d |
debug mode |
-v |
verbose mode |
-u |
normalize all input timeseries to unit variance |
-x<int> |
specify dimensionality of x process (default = 1) |
-m |
create text listing of AR model |
-w |
write residual after full AR modeling |
-P |
format residual output suitable for plotting (xyy) |
covariance
covariance, correlation, coherence, etc. on ASCII column data
Usage: covariance <format|fmtfile> <profile>
Examples:
covariance "4x124+" doubletask.txt
Options
-q |
quiet mode |
-t |
optionally remove trend (ramp) from input timeseries |
-u |
optionally normalize all input timeseries to unit variance |
-o |
output lagged CCV dat files (CCR with -u) |
-a |
output lagged ACV dat file (ACR with -u) |
-r |
output Bartlett smoothed cross spectra (spectral density with -u) |
-p |
output Bartlett smoothed auto spectra (spectral density with -u) |
-e |
compute eigenvectors of lag 0 CCV |
-L |
read ROI labels from <profile> (default ignore ‘#’ commented lines) |
-T<int> |
additionally smooth spectra with Tukey window of specified width (in frames) |
-d<flt> |
specify frame TR in sec for Fourier analysis (default = 1.0000) |
-m<int> |
specify CCV function maxumum lag in frames (default = 32) |
-D<flt> |
SVD lag 0 CCV and output new profile with cndnum < specified value (implies -e) |
-g<str> |
regress timeseries in named file out of <profile> |
N.B.: all input timeseries are made zero mean as a first step N.B.: region names can be specified on the first line of <profile> with ‘#’ in the first column