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jvs:fscan:manual:chapter1:cmdsummary
fScan Reference Manual, Chapter 1 (Topics): cmdsummary
Old 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:
jvs/fscan/manual/chapter1/cmdsummary.txt · Last modified: 2023/02/23 18:43 (external edit)
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