## Note: This page was created with the CommandTemplate
##
## If you're modifying this page please take a look at the
## latest version of CommandTemplate to ensure that you're
## using the latest version of the CommandTemplate
##
## See HelpOnCommandTemplate for description of formatting

<<Navigation(children)>>
'''Index'''
<<TableOfContents>>


= Name =
spatialsmooth-sess - 3D Gaussian [[Smoothing]] using [[FSL]] IP

= Synopsis =
spatialsmooth-sess -i instem -o outstem -fwhm FWHM -s sessid -d srchdir  [<options>] <<BR>>
spatialsmooth-sess -i instem -o outstem -fwhm FWHM -sf sessidfile -df srchdirfile [<options>]

= Arguments =
== Positional Arguments ==
none

== Required Flagged Arguments ==
|| -i instem  || input functional volume stem ||
|| -o outstem || output functional volume stem ||
|| -fwhm FWHM || gaussian fwhm (sigma = fwhm/2.36) ||
|| -s sessid or -sf sessidfile || ||
|| -d srchdir or -df srchdirfile || ||

== Optional Flagged Arguments ==
|| -fsd fsdir   || ||
|| -noinorm       || do not intensity norm smoothed volume ||
|| -umask umask || set unix file permission to [umask] ||
|| -version       || print version and exit ||
|| -help          || print help and exit ||

= Outputs =
|| outstem || ouput volume ||

= Description =
spatialsmooth-sess performs 3D Gaussian spatial [[Smoothing]] using the [[FSL]] IP program. It will operate on the input volume in each run. The output volume will be placed in the same directory. FWHM is the full-width, half-maximum of the spatial filter gaussian (sigma = fwhm/2.36).

= Examples =
== Example 1 ==
spatialsmooth-sess -s sessid -d sessdir -i fmc -o fmcsm5 -fwhm 5

Smooth the motion corrected volume with a gaussian kernel with FWHM of 5 mm. The result will be placed in the volume fmcsm5. This is the stem that should be referenced when creating the anlysis. It will also automatically run intensity normalization (ie, [[inorm-sess]]) for the smoothed volume unless -noinorm is specified.

== Example 2 ==
spatialsmooth-sess

description

= Bugs =
none

= See Also =
[[inorm-sess]]

= Links =
FsFast, [[FSL]]

= Methods Description =
{{{
The data were smoothed using a 3D Gaussian kernel with FWHM [FWHM]mm.
}}}

= References =
none

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =
DougGreve