fScan Reference Manual, Chapter 1 (Topics): cmdsummary
FScan command lines can accept a number of optional arguments, each indicated by an initial '-'. The following command line options are recognized:
-average | Generate average timecourse movie (with -M) |
-blocks | Specify block condition in 1 cycle |
-convolve | Convolve images using kernal matrix |
-cpus | Enable parallel process queuing |
-correlate | Generate map of correlation coefficients |
-despike | Filter extreme values (i.e., shot noise) |
-detrend | Remove slow temporal fluctuations (detrend) |
-display | Show images on window display (alias: -X) |
-expression | Do arithmetic expression using INFILE and IN2 |
-group | specify grouping parameters |
-header | File header specifications |
-history | Add file HIST to history; 0=omit history |
-join | Join (append) data in IN2 to INFILE |
-mask | Specify binary (byte) mask image for input |
-mean | Generate mean images |
-normalize | Normalize intensities to a constant mean |
-output | Create output file |
-options | Read command options from OPTIONFILE or menu |
-plot | Plot time data with uneven time base |
-phase | Create a phase map (with -F or -C) |
-reflist | Specify image reference codes |
-rfilter | Unmodulate temporal fluctuations by condition |
-rmap | Map temporal fluctuations by condition |
-recon | Reconstruct images from raw data |
-square | Clip to square images |
-subset | Specify XYZT subset |
-stabplots | Calculate displacements of center-of-mass |
-stats | Calculate ROI stats |
-surface | Surface data |
-timebase | Uneven TR; TR align/create T1 map/use T1 map to adjust |
-ttest | Generate ttest or simple threshold maps |
-verbose | Verbose flag – display progress information |
-variance | Generate variance images |
-writeover | Write over existing files flag |
-wait | Wait for input images to be generated |
Options:
-a flag width | Average input voxels in space or time |
-A file flag align gray flat | Anatomical images to use for background |
-b blk0 blk1 … blk9 | Duration of each block condition in 1 cycle |
-B flag arg0 arg1 … | Extra options describing condition blocks |
-c outfile hdrflg | Put a copy of raw input data to outfile |
-C ref out ptyp scal sav flg | Generate map of correlation coefficients |
-d out flag refimg slice max | Calculate displacements of center-of-mass |
-D nx ny nz nt wsz hdr rhdr… | Define data dimensions of input file |
-e [N] op in2 [mode] val val2 | Do arithmetic expression using INFILE and IN2 |
-E Nstdevs flg winsiz | Filter extreme values (i.e., shot noise) |
-f maxfreq flg out | Create a FFT frequency power spectrum |
-F freq out ptype fratio | Create a FFT power map at FREQ cycles |
-g grouptask maxgrps | Select grouping variable (for -M -V -T -A) |
-G flag t0 r1 r2 rt win n1 n2 | Get grouping codes from analog waveforms |
-h fmt [args] | File header format specifications |
-H hist | Add file HIST to history; 0=omit history |
-i ilist flg arg varb list2 | Specify input image codes |
-I gflg dxy oflg mode dt dbg | Reconstruct images from raw data |
-j cond1 cond2 … cond9 | Join conditions COND2 … with COND1 |
-J in2 flag | Join (append) data in IN2 to INFILE |
-k flg scale kernal offset | Convolve images using kernal matrix |
-K leng flg synch skp bin ref | Generate average timecourse movie (with -M) |
-l | |
-L | |
-m mask thresh_pct | Specify binary (byte) mask image for input |
-M out ptype maxvols ngroup | Generate mean images |
-n nx ny rdallflg | XY size of input subregion |
-N [nimgs nmlflg mean] | Normalize intensities to a constant mean |
-o x0 y0 | XY origin of input subregion |
-O optionfile | Read command options from OPTIONFILE or menu |
-p flag | Perturb alignment to find best overlap |
-P out max thrsh ptyp np dp p2 | Create a phase map (with -F or -C) |
-q | Clip to square images |
-Q nprocs procflg | Enable parallel process queuing |
-r flag x0 y0 z0 nx ny nz | Print ROI stats |
-R nnodes flag | Remove slow temporal fluctuations (detrend) |
-s scalfact ioff maxval flg | Specify scale and offset for output images |
-S [mode] file flag align … | Surface data |
-t t0 nt | T (volume) parameters of input subregion |
-T c1 c2 task out ptype thresh | Generate ttest or simple threshold maps |
-u trs t1map wrtflg t0 u0 | Uneven TR; TR align/create T1 map/use T1 map to adjust |
-U trec drec color flg y0 yscl | Plot time data with uneven time base |
-v level dbgflg dbgx dbgy … | Verbose flag – display progress information |
-V out ptype rdonly | Generate variance images |
-w wfile | Write flag |
-W flg | Wait for input images to be generated |
-x inorder outorder | Specify data order (default: in=xytz, out=in) |
-X dev flg panels tnam ncol… | Show images on X-window display |
-y cond flag nbins arg out | Map temporal fluctuations by condition |
-Y cond flag nbins arg | Unmodulate temporal fluctuations by condition |
-z z0 nz | Z parameters of input subregion |
-Z | Reslice image volume, or set slice flags |
See Also: