Differences between revisions 5 and 6

Name

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

Synopsis

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

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]

smoothed 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).

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

Author/s

DougGreve

Links

FsFast, ["FSL"]

References

None

Reporting Bugs

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

Methods Description

The data were smoothed using a 3D Gaussian kernel with FWHM [fwhm]mm.

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spatialsmooth-sess - 3D Gaussian smoothing using FSL IP

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+spatialsmooth-sess - 3D Gaussian ["Smoothing"] using ["FSL"] IP
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-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] 

}}}
+|| -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] || ||
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-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

}}}
+|| -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 ||
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-{{{     

volume1 - description

volume2 - description

}}}
+|| [outstem] || smoothed volume ||
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-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).
+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).
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-{{{
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-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.

}}}
+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.
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-}}}