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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 - 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 = |
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| 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. |
The data were smoothed using a 3D Gaussian kernel with FWHM [FWHM]mm. |
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| = Positional Arguments = {{{ |
= References = |
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| }}} = 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 = ## For example: ["Belliveau1991"] NameYear |
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| = Methods Description = ## Suitable for cutting and pasting into publication. ## No WikiLinks should be used. {{{ description description }}} = Category = ## For example: CategoryFreeSurferCommandVolumeConversion Category``Stream``Function |
= Author/s = DougGreve |
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>