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spatialsmooth-sess -i [instem] -o [outstem] -fwhm [gaussian fwhm (sigma = fwhm/2.36)] -s [sessid] or -sf [sessidfile]
-d [srchdir] or -df [srchdirfile] [<options>]
spatialsmooth-sess -i [instem] -o [outstem] -fwhm [gaussian fwhm (sigma = fwhm/2.36)] -s [sessid] '''or''' -sf [sessidfile]
-d [srchdir] '''or''' -df [srchdirfile] [<options>]

Name

spatialsmooth-sess 

Synopsis

spatialsmooth-sess -i [instem] -o [outstem] -fwhm [gaussian fwhm (sigma = fwhm/2.36)] -s  [sessid] '''or''' -sf [sessidfile] 
-d  [srchdir] '''or''' -df [srchdirfile] [<options>]

This program uses the FSL IP program to do 3D gaussian spatial smoothing (www.fmrib.ox.ac.uk/fsl). 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.

Positional Arguments

none

Required Flagged Arguments

   -i instem      : input  functional volume stem 

   -o outstem     : output functional volume stem 

   -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 mask

   -version        : print version and exit

   -help           : print help and exit

Outputs

volume1 - description
volume2 - description

Example 1

spatialsmooth-sess -s sessid -d sessdir -i fmc -o fmcsm5 -fwhm 5

This will 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.

description

Example 2

command foo -i f -o out -f fvalue

description

See Also

["othercommand1"], ["othercommand2"]

Author/s

JaneSmith

Links

FreeSurfer, FsFast

Description

description

References

NameYear

Reporting Bugs

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

Methods Description

description
description

Category

CategoryStreamFunction

spatialsmooth-sess (last edited 2008-04-29 11:45:26 by localhost)