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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 |
Index
Contents
Name
spatialsmooth-sess - 3D Gaussian Smoothing using FSL IP
Synopsis
spatialsmooth-sess -i instem -o outstem -fwhm FWHM -s sessid -d srchdir [<options>]
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
Links
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>