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## If you are modifying this page please take a look at the ## CommandTemplate page and check that this page has the latest ## CommandTemplate formatting |
## Note: This page was created with the CommandTemplate ## ## If you're modifying this page please take a look at the ## latest version of CommandTemplate to ensure that you're ## using the latest version of the CommandTemplate ## ## See HelpOnCommandTemplate for description of formatting [[Navigation(children)]] '''Index''' [[TableOfContents]] |
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| spatialsmooth-sess -i [instem] -o [outstem] -fwhm [fwhm] -s [sessid] or -sf [sessidfile] -d [srchdir] or -df [srchdirfile] [<options>] |
spatialsmooth-sess -i instem -o outstem -fwhm FWHM -s sessid -d srchdir [<options>] [[BR]] spatialsmooth-sess -i instem -o outstem -fwhm FWHM -sf sessidfile -df srchdirfile [<options>] |
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| = Positional Arguments = |
= Arguments = == Positional Arguments == |
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= 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] || || |
== 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 || || |
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= Optional Flagged Arguments = || -fsd [fsdir] || || |
== Optional Flagged Arguments == || -fsd fsdir || || |
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| || -umask [umask] || set unix file permission to [umask] || | || -umask umask || set unix file permission to [umask] || |
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| || [outstem] || smoothed volume || | || outstem || ouput volume || |
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| = Example 1 = |
= Examples = == Example 1 == |
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| = Example 2 = | == Example 2 == |
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= Bugs = none |
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| The data were smoothed using a 3D Gaussian kernel with FWHM [fwhm]mm. | The data were smoothed using a 3D Gaussian kernel with FWHM [FWHM]mm. |
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Navigation(children) Index TableOfContents
Name
spatialsmooth-sess - 3D Gaussian ["Smoothing"] using ["FSL"] IP
Synopsis
spatialsmooth-sess -i instem -o outstem -fwhm FWHM -s sessid -d srchdir [<options>] BR spatialsmooth-sess -i instem -o outstem -fwhm FWHM -sf sessidfile -df srchdirfile [<options>]
Arguments
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 |
ouput 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).
Examples
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
Bugs
none
See Also
["inorm-sess"]
Links
FsFast, ["FSL"]
Methods Description
The data were smoothed using a 3D Gaussian kernel with FWHM [FWHM]mm.
References
none
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>