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| ## see dtrecon as an exmaple | ## See HelpOnCommandTemplate for description of formatting ## ## Note: If you are modifying this page please refer to the ## CommandTemplate page and confirm that this page has the latest ## CommandTemplate formatting |
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| mc-sess - MotionCorrection using ["AFNI"] = Synopsis = mc-sess -s [sessid] -d [srchdir] [<options>] [[BR]] mc-sess -sf [sessidfile] -df [srchdirfile] [<options>] = Positional Arguments = None = Required Flagged Arguments = || -s [sessid] or -sf [sessidfile] || description || || -d [srchdir] or -df [srchdirfile] || description || = Optional Flagged Arguments = || -method [mcmethod] || afni || || -targnthrun [n] || uses [nth] run as target. default: [n]=1 || || -toff [m] || [m] is target image offset || || -fstem [outstem] || stem of output motion-corrected volume (fmc) || || -fmcstem [outstem] || stem of output motion-corrected volume (fmc) || || -umask [umask] || set unix file permission mask to [umask] || || -version || print version and exit || || -rlf [runlistfile] || only process those in the [runlist] file || = Outputs = || [outstem] || motion-corrected volume || = Description = mc-sess performs MotionCorrection using the ["AFNI"] MotionCorrection tool. By default, the MotionCorrection is performed to the first run, although you can motion correct to a different run using the -targnthrun flag. = Example 1 = mc-sess -s grp1id -d grp1dir mc-sess using sess id and a search directory = Example 2 = mc-sess -sf grp1sessfile -df grp1dirfile mc-sess using sess id file and search directory file = See Also = ["othercommand1"], ["othercommand2"] = Links = FsFast, FsFastMotionCorrection, ["AFNI"] = Methods Description = |
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| mc-sess - motion correction using AFNI }}} = Synopsis = {{{ mc-sess arg1 -i <arg2> -o <arg3> [<options>] |
The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/). |
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| = Positional Arguments = {{{ arg1 description }}} |
= References = References/Cox1999 |
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| = Required Flagged Arguments = {{{ -i <arg2> description -o <arg3> description }}} = Optional Flagged Arguments = {{{ -f <fvalue> description description -g <gvalue> description description }}} = Outputs = {{{ volume1 - description volume2 - description }}} = Example 1 = {{{ mc-sess foo -i f -o out }}} = Example 2 = {{{ mc-sess foo -i f -o out -f fvalue }}} = See Also = ["othercommand1"], ["othercommand2"] |
= Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> |
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| DougGreve | DougGreve |
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| = Links = FsFast, FsFastMotionCorrection, ["AFNI"] = References = ## For example: ["Belliveau1991"] NameYear = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFsFastCommandsMotionCorrection |
Name
mc-sess - MotionCorrection using ["AFNI"]
Synopsis
mc-sess -s [sessid] -d [srchdir] [<options>] BR mc-sess -sf [sessidfile] -df [srchdirfile] [<options>]
Positional Arguments
None
Required Flagged Arguments
-s [sessid] or -sf [sessidfile] |
description |
-d [srchdir] or -df [srchdirfile] |
description |
Optional Flagged Arguments
-method [mcmethod] |
afni |
-targnthrun [n] |
uses [nth] run as target. default: [n]=1 |
-toff [m] |
[m] is target image offset |
-fstem [outstem] |
stem of output motion-corrected volume (fmc) |
-fmcstem [outstem] |
stem of output motion-corrected volume (fmc) |
-umask [umask] |
set unix file permission mask to [umask] |
-version |
print version and exit |
-rlf [runlistfile] |
only process those in the [runlist] file |
Outputs
[outstem] |
motion-corrected volume |
Description
mc-sess performs MotionCorrection using the ["AFNI"] MotionCorrection tool. By default, the MotionCorrection is performed to the first run, although you can motion correct to a different run using the -targnthrun flag.
Example 1
mc-sess -s grp1id -d grp1dir
mc-sess using sess id and a search directory
Example 2
mc-sess -sf grp1sessfile -df grp1dirfile
mc-sess using sess id file and search directory file
See Also
["othercommand1"], ["othercommand2"]
Links
FsFast, FsFastMotionCorrection, ["AFNI"]
Methods Description
The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/).
References
References/Cox1999
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>