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| 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 = 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 = {{{ 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 |
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| ## 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 |
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
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>