**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:

|[[jvs:fscan:manual:chapter1:cmdsummary:average|-average]]|Generate average timecourse movie (with -M)|
|[[jvs:fscan:manual:chapter1:cmdsummary:blocks|-blocks]]|Specify block condition in 1 cycle|
|[[jvs:fscan:manual:chapter2:convolve|-convolve]]|Convolve images using kernal matrix|
|[[jvs:fscan:manual:chapter2:cpus|-cpus]]|Enable parallel process queuing|
|[[jvs:fscan:manual:chapter1:cmdsummary:correlate|-correlate]]|Generate map of correlation coefficients|
|[[jvs:fscan:manual:chapter2:despike|-despike]]|Filter extreme values (i.e., shot noise)|
|[[jvs:fscan:manual:chapter1:cmdsummary:detrend|-detrend]]|Remove slow temporal fluctuations (detrend)|
|[[jvs:fscan:manual:chapter2:display|-display]]|Show images on window display (alias: -X)|
|[[jvs:fscan:manual:chapter2:expression|-expression]]|Do arithmetic expression using INFILE and IN2|
|[[jvs:fscan:manual:chapter2:group|-group]]|specify grouping parameters|
|[[jvs:fscan:manual:chapter2:header|-header]]|File header specifications|
|[[jvs:fscan:manual:chapter2:history|-history]]|Add file HIST to history; 0=omit history|
|[[jvs:fscan:manual:chapter2:join|-join]]|Join (append) data in IN2 to INFILE|
|[[jvs:fscan:manual:chapter2:mask|-mask]]|Specify binary (byte) mask image for input|
|[[jvs:fscan:manual:chapter2:mean|-mean]]|Generate mean images|
|[[jvs:fscan:manual:chapter2:normalize|-normalize]]|Normalize intensities to a constant mean|
|[[jvs:fscan:manual:chapter2:output|-output]]|Create output file|
|[[jvs:fscan:manual:chapter2:options|-options]]|Read command options from OPTIONFILE or menu|
|[[jvs:fscan:manual:chapter2:plot|-plot]]|Plot time data with uneven time base|
|[[jvs:fscan:manual:chapter2:phase|-phase]]|Create a phase map (with -F or -C)|
|[[jvs:fscan:manual:chapter1:cmdsummary:reflist|-reflist]]|Specify image reference codes|
|[[jvs:fscan:manual:chapter1:cmdsummary:rfilter|-rfilter]]|Unmodulate temporal fluctuations by condition|
|[[jvs:fscan:manual:chapter1:cmdsummary:rmap|-rmap]]|Map temporal fluctuations by condition|
|[[jvs:fscan:manual:chapter1:cmdsummary:recon|-recon]]|Reconstruct images from raw data|
|[[jvs:fscan:manual:chapter1:cmdsummary:square|-square]]|Clip to square images|
|[[jvs:fscan:manual:chapter2:subset|-subset]]|Specify XYZT subset|
|[[jvs:fscan:manual:chapter1:cmdsummary:stabplots|-stabplots]]|Calculate displacements of center-of-mass|
|[[jvs:fscan:manual:chapter2:stats|-stats]]|Calculate ROI stats|
|[[jvs:fscan:manual:chapter2:surface|-surface]]|Surface data|
|[[jvs:fscan:manual:chapter2:timebase|-timebase]]|Uneven TR; TR align/create T1 map/use T1 map to adjust|
|[[jvs:fscan:manual:chapter2:ttest|-ttest]]|Generate ttest or simple threshold maps|
|[[jvs:fscan:manual:chapter2:verbose|-verbose]]|Verbose flag -- display progress information|
|[[jvs:fscan:manual:chapter1:cmdsummary:variance|-variance]]|Generate variance images|
|[[jvs:fscan:manual:chapter2:writeover|-writeover]]|Write over existing files flag|
|[[jvs:fscan:manual:chapter2:wait|-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|fScan Home]], 
[[jvs:fscan:manual|fScan Manual]], 
[[jvs:fscan:manual:chapter1|Topics]], 
[[jvs:fscan:manual:help|Manual Help]]