| Deletions are marked like this. | Additions are marked like this. |
| Line 7: | Line 7: |
| spatialsmooth-sess | spatialsmooth-sess - 3D Gaussian smoothing using FSL IP |
| Line 9: | Line 9: |
| Line 11: | Line 12: |
|
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. |
spatialsmooth-sess -i [instem] -o [outstem] -fwhm [fwhm] -s [sessid] or -sf [sessidfile] -d [srchdir] or -df [srchdirfile] [<options>] |
| Line 26: | Line 22: |
| -i instem : input functional volume stem |
-i instem input functional volume stem |
| Line 28: | Line 25: |
| -o outstem : output functional volume stem |
-o outstem output functional volume stem |
| Line 30: | Line 28: |
| -fwhm : gaussian fwhm (sigma = fwhm/2.36) |
-fwhm gaussian fwhm (sigma = fwhm/2.36) |
| Line 32: | Line 31: |
| -s [sessid] or -sf [sessidfile] | -s [sessid] or -sf [sessidfile] |
| Line 34: | Line 33: |
|
-d [srchdir] or -df [srchdirfile] |
-d [srchdir] or -df [srchdirfile] |
| Line 40: | Line 38: |
| -fsd [fsdir] | -fsd [fsdir] |
| Line 42: | Line 40: |
| -noinorm : do not intensity norm smoothed volume |
-noinorm do not intensity norm smoothed volume |
| Line 44: | Line 43: |
| -umask umask : set unix file permission mask |
-umask umask set unix file permission to [umask] |
| Line 46: | Line 46: |
| -version : print version and exit |
-version print version and exit |
| Line 48: | Line 49: |
|
-help : print help and exit |
-help print help and exit |
| Line 58: | Line 59: |
|
= 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). |
|
| Line 62: | Line 67: |
|
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 |
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. |
| Line 71: | Line 72: |
| command foo -i f -o out -f fvalue | spatialsmooth-sess |
| Line 77: | Line 78: |
| ["othercommand1"], ["othercommand2"] | ["inorm-sess"] |
| Line 80: | Line 81: |
| JaneSmith | DougGreve |
| Line 83: | Line 84: |
|
FreeSurfer, FsFast = Description = description |
FsFast, ["FSL"] |
| Line 89: | Line 87: |
|
## For example: ["Belliveau1991"] NameYear |
None |
| Line 96: | Line 93: |
|
## Suitable for cutting and pasting into publication. ## No WikiLinks should be used. |
|
| Line 99: | Line 94: |
|
description description |
The data were smoothed using a 3D Gaussian kernel with FWHM [fwhm]mm. |
| Line 104: | Line 98: |
|
## For example: CategoryFreeSurferCommandVolumeConversion Category``Stream``Function |
CategoryFsFastCommandsSmoothing |
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 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
volume1 - description volume2 - description
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"]
Author/s
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.