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## CommandTemplate formatting

= Name =
mkbrainmask-sess - make brain mask using [[BET]]

= Synopsis =
mkbrainmask-sess -s [sessid] -d [srchdir] [<options>] <<BR>>
mkbrainmask-sess -sf [sessidfile] -df [srchdirfile]  [<options>]

= Positional Arguments =
None

= Required Flagged Arguments =
|| -s [sessid] or -sf [sessidfile]   || description ||
|| -d [srchdir] or -df [srchdirfile] || description ||

= Optional Flagged Arguments =
||  -fsd   [funcsubdir]  ||  functional subdirectory (default: bold) ||
||  -run  [nth]          ||  use the nth run (default is 1st) ||
||  -thresh  [threshold] ||  fraction of global mean to separate brain and air (default is .1) ||
||  -maskstem stem       ||  stem of binary mask (stored in fsd/masks/stem) default is brain ||
|| -help                 ||  print help and exit ||
|| -version              ||  print version and exit ||

= Outputs =
|| volume1 || description ||

= Description =
mkbrainmask-sess creates a binary mask of the brain from an input functional volume. It uses the [[FSL]] Brain Extraction Tool ([[BET]]). By default, the input is the f volume from the first run of the session from the bold directory.  The input volume can be changed with the -funcstem option; the run can be changed with the -run option; and the functional subdirectory can be changed with the -fsd option. The output will be placed in a directory called masks under the FSD. The stem will be brain unless changed with the -maskstem option. The only real parameter is the threshold (controlled with the -thresh option). The absolute threshold is set to thresh times the global mean.

= Example 1 =
mkbrainmask-sess foo -i f -o out

description

= Example 2 =
mkbrainmask-sess foo -i f -o out -f fvalue

description

= See Also =
[[othercommand1]]

= Links =
FsFast, [[FSL]], SkullStripping

= Methods Description =
{{{
A brain mask was generated using the Brain 
Extraction Tool (BET) which is available from
the FSL software library (www.fmrib.ox.ac.uk/fsl) (Smith 2002).
}}}

= References =
[[References/Smith2002]]

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

= Author/s =
DougGreve