Name

mkbrainmask-sess - make brain mask using BET

Synopsis

mkbrainmask-sess -s [sessid] -d [srchdir] [<options>]
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