.. include:: ../global.rst Evaluate and ROI-oriented programs ================================== peak_4dfp --------- locate and consolidate maxima to generate ROI Usage: peak_4dfp Examples:: peak_4dfp grand_average_222[.4dfp.img] -s10 Options ================ =========================================================================================== -s preblur with hard sphere kernel of specified radius (invokes hsphere_4dfp) -n limit initial pos and neg peak list lengths (default=1000) -c[to] specify sign inverted curvature thresholds (default none) -v[to] specify peak value thresholds (default none) -d consolidate extremum pairs closer than specified distance -o output a fidl compatible 4dfp format ROI file with regions of specified radius -m apply named mask file to output ROIs -N specify output ROI minimum voxel count (default = 1) -a append specified string to ROI output filename -q quiet mode (suppress rec file listing) -F force preblur image creation even if hsphere_4dfp result exists (no effect without -s) -@ output big or little endian (default input endian) ================ =========================================================================================== N.B.: operations controlled by options -s, -n, -c, -v, -d, -o, -m, -N are applied serially in listed order |br| N.B.: all distances are in mm read_4dfp --------- report value of image at specified real coordinate Usage: read_4dfp <4dfp imgroot> [options] Examples:: read_4dfp 33.1 -56.2 18. grand_average_222[.4dfp.img] Options == ============ -v verbose mode == ============ imgmax_4dfp ----------- report maximum and minimum values Usage: imgmax_4dfp Options == ============================================ -m report min as well as max -e report max/min values in scientific notation -r report root sum of squares -v verbose (time series) mode == ============================================ img_hist_4dfp ------------- construct voxel value histogram; evaluate moments Usage: img_hist_4dfp <(4dfp) image> Options ================ ============================================================================ -b specify number of bins (default = 100) -f select volume (counting from 1) of 4dfp stack (default analyze all volumes) -t specify image intensity threshold -r[to] specify histogram range -m<(4dfp) mask> mask input using (non-zero voxels of) specified mask (only first frame used) -h create .hist file suitable for plotting, e.g., with xmgr -p create .dat file suitable for input to numerical procedures -x create .xtile percentile listing -C create output files in $cwd (default parallel to <(4dfp) image>) -u normalize output .hist and .dat distributions to unit area -s report moments ================ ============================================================================ N.B.: option -f causes selected volume to be reported in filename of -{hpx} created files .. _qnt_4dfp: qnt_4dfp -------- report mean value within 3D ROI Usage: qnt_4dfp <(4dfp)|(conc) image> <(4dfp) mask> Examples:: qnt_4dfp -t23.2 va1234_mpr mask Options ================ =============================================================================================== -s time series mode -d include backwards differences (differentiated signal) in output (requires -f or -F, implies -s) -D count only defined (finite, non 0.0, non-NaN, non 1.e-37) voxels -A apply threshold test to absolute value of -W interpret as spatial weights (negative values allowed) (disables mask threshold testing) -v[to] count only voxels within specified range -f specify frames to count format, e.g., "4x120+4x76+" -F read frames-to-count format from specified file -p specify mask threshold as percent of max -t specify absolute threshold (default = 0.0) -c scale output mean values by specified constant (default = 1.0) ================ =============================================================================================== N.B.: only the first frame of is used |br| N.B.: and may be the same |br| N.B.: conc files must have extension "conc" .. _qntm_4dfp: qntm_4dfp --------- evaluate multiple volumes in multiple ROIs Usage: qntm_4dfp <(4dfp)|(conc) image> <(4dfp) ROI> Examples:: qntm_4dfp TC30274_rmsp_faln_dbnd_xr3d_atl.conc iter10_roi_-02_-37_+27m_ROI Options ======= ======================================================= -Z count zero voxels in as defined -V force code_by_volume even if the number of volumes is 1 -N create ROIs/voxel image -o write output to specified text file (default stdout) -h suppress printing output header ======= ======================================================= N.B.: conc files must have extension "conc" |br| N.B.: only defined voxels (not 0.0 and not NaN and not 1.e-37 and finite) are counted |br| N.B.: <(4dfp) ROI> may either a value-coded single volume ROI image or a multi-volume mask |br| N.B.: <(4dfp) ROI> coded values are integerized |br| N.B.: qntm_4dfp ignores <(4dfp) ROI> ifh center and mmppix fields .. _qntv_4dfp: qntv_4dfp --------- evaluate multiple volumes in ROI subdivided into cubes Usage: qntv_4dfp <(4dfp)|(conc) image> <(4dfp) ROI> Examples:: qntv_4dfp TC30274_rmsp_faln_dbnd_xr3d_atl.conc iter10_roi_-02_-37_+27m_ROI Options ======= ==================================================================================== -H include header info in output -V print defined voxel counts per die -D create die image (voxels >= ncrit) -K create die (voxel) coordinate listing -Z count zero voxels in as defined -O select output type (see below) -f specify frames-to-count format (default count all frames) -F read frames-to-count format from specified file (supersedes option -f) -l specify length of die in voxels (default 1) -n specify minimum die voxel count (default 1) -t specify svd output tolerance - ratio of least to greatest eigenvalue (default 1e-06) -o write output to specified text file (default stdout) ======= ==================================================================================== -O options = ========================================================== 1 timeseries directly extracted from dice 2 timeseries extracted from dice with mean removed 3 die timeseries passed through svd multiplied by eigenvalue 4 die timeseries passed through svd (unit variance) = ========================================================== N.B.: conc files must have extension "conc" |br| N.B.: only defined voxels (not 0.0 and not NaN and not 1.e-37 and finite) are counted |br| N.B.: qntv_4dfp ignores <(4dfp) ROI> ifh center and mmppix fields |br| N.B.: to obtain a GLM condition number = X specificy sqrt(1/X) as tol with option -t qntw_4dfp --------- evaluate multiple volumes using weighted ROI Usage: qntw_4dfp <(4dfp)|(conc) image> <(4dfp) ROI> Examples:: qntw_4dfp TC30274_rmsp_faln_dbnd_xr3d_atl.conc iter10_roi_-02_-37_+27m_ROI Options ======= ==================================================== -L specify ROI weight L-norm (default = 0) -o write output to specified text file (default stdout) -Z count zero voxels in as defined -H include heaer info in output ======= ==================================================== N.B.: conc files must have extension "conc" |br| N.B.: <(4dfp) ROI> is interpreted as a multi-volume voxel-wise set of weights |br| N.B.: only defined voxels (not 0.0 and not NaN and not 1.e-37 and finite) are counted |br| N.B.: qntw_4dfp ignores <(4dfp) ROI> ifh center and mmppix fields .. _var_4dfp: var_4dfp -------- evaluate variance or s.d. about mean over timeseries Usage: var_4dfp <(4dfp|conc) input> Examples:: var_4dfp -sn3 -c10 test_b1_rmsp_dbnd Options ======= ================================================================== -d debug mode -m remove mean volume from stack -s compute s.d. about mean -G compute mean ignoring run boundaries (default within runs) -v compute variance about mean (default operation) -z output logical and of all defined voxels -n specify number of pre-functional frames per run (default = 0) -f specify frames to count format, e.g., "4x120+4x76+" (overrides -n) -F read format from specified file -c scale output image values by specified factor -N output undefined voxels as NaN -Z output undefined voxels as 0 -E output undefined voxels as 1.e-37 (default) -@ output big or little endian (default input endian) ======= ================================================================== N.B.: input conc files must have extension "conc" |br| N.B.: identically zero input voxels are counted as defined |br| N.B.: options {-v -s -m -z} are mutually exclusive |br| N.B.: absent -G voxelwise mean is individually computed over each run in conc |br| N.B.: -f option overrides -n .. _dvar_4dfp: dvar_4dfp --------- evaluate variance or s.d. about mean over differentiated timeseries Usage: dvar_4dfp [options] Examples:: dvar_4dfp -n3 test_b1_rmsp_dbnd -mtest_anat_ave_mskt Options =============== ================================================== -m<(4dfp) mask> use specified 4dfp mask -n specify number of pre-functional (anatomy) frames -t specify maskfile threshold (default = 0.0) -b specify preblur FWHM in mm (default none) -s output sqrt(dvar) (default dvar) -@ output big or little endian (default input endian) =============== ================================================== burn_sphere_4dfp ---------------- “burn in” sphere at specified real coordinates Usage: burn_sphere_4dfp <4dfp imgroot> <4dfp outroot> [options] Examples:: burn_sphere_4dfp 33.1 -56.2 18. grand_average_222[.4dfp.img] -v2 -o7.5 burn_sphere_4dfp 33.1 -56.2 18. 222 -v2 -o7.5 Options ======= ==================================================================================== -a superimpose sphere on image (default duplicate input format with zero background) -s sum overlapping spheres (default overwrite) -v specify burn in value (default=1.0000) -o specify sphere radius in mm (default=6.0000) (radius of 0 creates single pixel burn) -l read sphere coordinates from specified list (command line coords ignored) -@ output big or little endian (default input endian) ======= ==================================================================================== N.B.: without -a only the input ifh (or standard atlas string) is required |br| N.B.: specifying <4dfp imgroot> as "333[.n]" "222" or "111" generates standard atlas space output |br| N.B.: if the 4dfp image does not exist the default output endianness is CPU endian ROI_resolve_4dfp ---------------- resolve a set of possibly overlapping ROIs into a disjoint set Usage: ROI_resolve_4dfp <(4dfp) ROI1> <(4dfp) ROI2> <(4dfp) ROI3> ... Options ======= ================================================ -l read input file names from specified list file -@ output big or little endian (default CPU endian) ======= ================================================ N.B.: output 4dfp fileroots are same as inputs with appended "z" imgsurf_4dfp ------------ move ROI coordinates to nearest surface Usage: imgsurf_4dfp <(4dfp) image> N.B.: lists loci in atlas coordinates (X Y Z) in mm spatial_corr_4dfp ----------------- compute image similarity as correlation over space Usage: spatial_corr_4dfp [output_text_file] Options ======= ========================================================= -C compute covariance (default correlation) -M suppress removal of patial means -c scale output covariance matrix values by specified factor ======= ========================================================= N.B.: image dimensions must match |br| N.B.: spatial_corr_4dfp counts only defined (not NaN or 1.e-37 or 0.0) voxels spatial_cov_multivol_4dfp ------------------------- compute volume-pair covariance over space Usage: spatial_cov_multivol_4dfp <(4dfp) image> <(4dfp) mask> Options ======= ================================================================ -Z compute covariance with respect to zero (default wrt image mean) -p generate specified number of PCs (default none) -c scale text output covariance matrix values by specified factor ======= ================================================================ N.B.: spatial_cov_multivol_4dfp counts only defined (not NaN or 1.e-37) voxels |br| N.B.: zero voxels are counted as defined in <(4dfp) image> in cov computation |br| N.B.: zero voxels are counted as undefined in <(4dfp) image> in <(4dfp) mask> |br| N.B.: all zero or all undefined <(4dfp) image> volumes are ignored