**fScan Reference Manual, Chapter 2 (CmdLineOptions): set**
===== Set -- Set parameter values =====
====usage: -set SETNAME ARG(s) ====

The SET command can be used to set control parameters, load special data values, or to create user-defined parameter variables.  The first word (SETNAME) following the "-set" command specifies what the command will do.

The [[jvs:fscan:manual:chapter2:config|CONFIG]] command is the same as the SET command, except that CONFIG values will be set prior to executing any other processing commands (SET commands are processed with other commands and may therefore not have the intended effect).

Options are:

|**Name**|**Description**|
|[[jvs:fscan:manual:chapter2:setuservarb|accept]]|Set a user variable interactively |
|[[jvs:fscan:manual:chapter2:setactive|active]]|Set |
|[[jvs:fscan:manual:chapter2:setalert|alert]]|Set |
|[[jvs:fscan:manual:chapter2:setallscale|allscale]]|Set |
|[[jvs:fscan:manual:chapter2:setautoview|autoview]]|Set |
|[[jvs:fscan:manual:chapter2:setcolor|colorNN]]|Set color variable (N=1-3)|
|[[jvs:fscan:manual:chapter2:setcolormap|colormap]]|Set |
|[[jvs:fscan:manual:chapter2:setconvolve|convolve]]|Set the temporal response convolution kernel|
|[[jvs:fscan:manual:chapter2:setcopymaskbits|copymaskbits]]|Set |
|[[jvs:fscan:manual:chapter2:setdatafile|datafile]]|Set |
|[[jvs:fscan:manual:chapter2:setdatapath|datapath]]|Set |
|[[jvs:fscan:manual:chapter2:setdatasetname|datasetname]]|Set the logical name for the current data set|
|[[jvs:fscan:manual:chapter2:setdatatype|datatype]]|Set |
|[[jvs:fscan:manual:chapter2:setdesign|design]]|Set |
|[[jvs:fscan:manual:chapter2:setdicomtemplate|dicomtemplate]]|Set |
|[[jvs:fscan:manual:chapter2:setdiscard|discard]]|Set |
|[[jvs:fscan:manual:chapter2:setdisplayscale|displayscale]]|Set |
|[[jvs:fscan:manual:chapter2:setfilename|filename]]|Set |
|[[jvs:fscan:manual:chapter2:setflirtmtx|flirtmtx]]|Set |
|[[jvs:fscan:manual:chapter2:setfont|font]]|Set |
|[[jvs:fscan:manual:chapter2:setfscanlog|fscanlog]]|Set |
|[[jvs:fscan:manual:chapter2:setglossary|glossary]]|Set |
|[[jvs:fscan:manual:chapter2:sethrdelay|hrdelay]]|Set the hemodynamic delay variable|
|[[jvs:fscan:manual:chapter2:seticon|icon]]|Set an icon image file name|
|[[jvs:fscan:manual:chapter2:setimageformat|imageformat]]|Set the default snapshot file format|
|[[jvs:fscan:manual:chapter2:setimagename|imagename]]|Set the snapshot file name prefix|
|[[jvs:fscan:manual:chapter2:setinset|inset]]|Control inset image options |
|[[jvs:fscan:manual:chapter2:setlink|linkedfile]]|Link a related file to this data set |
|[[jvs:fscan:manual:chapter2:setlist|list]]|Set |
|[[jvs:fscan:manual:chapter2:setloc|locN]]|Set location variable (N=1-3) to an XYZ position|
|[[jvs:fscan:manual:chapter2:setlutscale|lutscale]]|Set |
|[[jvs:fscan:manual:chapter2:setmainflag|mainflag]]|Set |
|[[jvs:fscan:manual:chapter2:setmainwidth|mainwidth]]|Set Main menu text width|
|[[jvs:fscan:manual:chapter2:setmap|map]]|Set a color map|
|[[jvs:fscan:manual:chapter2:setmaptype|maptype]]|Set |
|[[jvs:fscan:manual:chapter2:setmargins|margins]]|Set |
|[[jvs:fscan:manual:chapter2:setmatrix|matrix]]|Set |
|[[jvs:fscan:manual:chapter2:setmenuflag|menuflag]]|Set |
|[[jvs:fscan:manual:chapter2:setname|name]]|Set |
|[[jvs:fscan:manual:chapter2:setuservarb|number]]|Set a user-defined number variable|
|[[jvs:fscan:manual:chapter2:setoutformat|outformat]]|Set the default output file format|
|[[jvs:fscan:manual:chapter2:setoverwrite|overwrite]]|Set the Overwrite flag|
|[[jvs:fscan:manual:chapter2:setparam|param]]|Set |
|[[jvs:fscan:manual:chapter2:setpdigmfile|pdigmfile]]|Set the associated paradigm data file name|
|[[jvs:fscan:manual:chapter2:setquitconfirm|quitconfirm]]|Set |
|[[jvs:fscan:manual:chapter2:setquitstr|quitstr]]|Set |
|[[jvs:fscan:manual:chapter2:setregister|register]]|Set |
|[[jvs:fscan:manual:chapter2:setrtdxyzval|rtdxyzval]]|Set |
|[[jvs:fscan:manual:chapter2:setrtdxyzwin|rtdxyzwin]]|Set |
|[[jvs:fscan:manual:chapter2:setschedule|schedule]]|Set an associated task-timeing schedule file|
|[[jvs:fscan:manual:chapter2:setshowpanes|showpanes]]|Set |
|[[jvs:fscan:manual:chapter2:setshowtext|showtext]]|Set |
|[[jvs:fscan:manual:chapter2:setshowzoom|showzoom]]|Set |
|[[jvs:fscan:manual:chapter2:setuservarb|string]]|Set a user-defined string variable|
|[[jvs:fscan:manual:chapter2:setsubtype|subtype]]|Set |
|[[jvs:fscan:manual:chapter2:setsurfsubject|surfsubject]]|Set the (FreeSurfer) subject name|
|[[jvs:fscan:manual:chapter2:setsysvarb|sysvarb]]|Set |
|[[jvs:fscan:manual:chapter2:settaskbar|taskbar]]|Set |
|[[jvs:fscan:manual:chapter2:settaskname|taskname]]|Set |
|[[jvs:fscan:manual:chapter2:settempdir|tempdir]]|Set |
|[[jvs:fscan:manual:chapter2:settextflag1|textflag1]]|Set |
|[[jvs:fscan:manual:chapter2:settextflag2|textflag2]]|Set |
|[[jvs:fscan:manual:chapter2:setthumbsize|thumbsize]]|Set |
|[[jvs:fscan:manual:chapter2:settopblank|topblank]]|Set TOPBLANK pixels to 0 at the top of each window|
|[[jvs:fscan:manual:chapter2:setuservarb|USERNAME]]|Set user-defined variable USERNAME|
|[[jvs:fscan:manual:chapter2:setxml|xml]]|Load settings from an XML file|

  * colorN COLOR - set color variable (N=1-3) to the indicated color. COLOR can be a [[jvs:fscan:manual:colornames|color name]], a 24 bit [[jvs:fscan:manual:colorvalue|color value]], or the word 'taskbar' in which case the color will be taken from the most recent pixel clicked in the Taskbar window.
  * convolve NAME - Set the response convolution kernel to the named time series reference (see the [[jvs:fscan:manual:chapter2:reference|reference]] command for more about time series data).  This also activates the convolution flag. When convolution is active, fMRI task reference functions used in are convolved by the kernel before performing correlations.
  * convolve FLAG - Control activation of convolution kernel (0=inactivate, 1:activate). This is ignored if no kernel has been named.
  * hrdelay SECS - set latency offset to use in fMRI time series analyses
  * icon - set icon string
  * imageformat FMT - set format flag for window [[jvs:fscan:manual:chapter3:winkeys:snapshot|snapshots]] ('tiff' or 'jpeg')

  * imagename NAME - set filename prefix for window [[jvs:fscan:manual:chapter3:winkeys:snapshot|snapshots]]

  * inset DATANAME DELAY LOC DT SCALE START - set inset parameters for merging reference images into time series movies created using the [[jvs:fscan:manual:chapter3:imagekeys:adjust|ADJUST]] command.  Refer to that command for details about the inset arguments.  Inset values remain in effect until turned off (see next line).
  * inset 0 - turn off inset settings
  * linkedfile LINKTYPE FILENAME [BROWSESTRING] - link a related file
  * locN X Y Z - set location variable (N=1-3) to explicit X,Y,Z values

  * map NAME - set color map name (use "-set map name 1" to see map image)
  * matrix - set align matrix file name (unused?)

  * outformat FMT - set default data file [[jvs:fscan:manual:chapter2:output|output]] format
  * overwrite FLAG - set file overwrite flag (0=no, 1=yes)
  * pdigmfile [FILENAME [BROWSESTRING]]- set the current dataset's behavioral paradigm file name (e.g. CIGAL pdigm file)
  * surfsubject SUBJNAME - set subject name for surface data files (e.g. FreeSurfer subject name)
  * xml FILENAME - read values from named file
	
**See Also:**\\
[[jvs:fscan:manual:chapter2:config|Config]]

[[jvs:fscan|fScan Home]], 
[[jvs:fscan:manual|fScan Manual]], 
[[jvs:fscan:manual:chapter2|CmdLineOptions]], 
[[jvs:fscan:manual:help|Manual Help]]