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