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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 - motion correction using AFNI }}} |
mc-sess - motion correction using ["AFNI"] |
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| {{{ mc-sess arg1 -i <arg2> -o <arg3> [<options>] }}} |
mc-sess -s [sessid] or -sf [sessidfile] -d [srchdir] or -df [srchdirfile] [<options>] |
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| {{{ arg1 description }}} |
None |
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| {{{ -i <arg2> description -o <arg3> description }}} |
|| -s [sessid] or -sf [sessidfile] || description || || -d [srchdir] or -df [srchdirfile] || description || |
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| {{{ -f <fvalue> description description -g <gvalue> description description }}} |
|| -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 || |
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| {{{ volume1 - description volume2 - description }}} |
|| [outstem] || motion-corrected volume || |
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| {{{ mc-sess foo -i f -o out }}} |
mc-sess -s grp1id -d grp1dir mc-sess using sess id and a search directory |
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| {{{ mc-sess foo -i f -o out -f fvalue }}} |
mc-sess -sf grp1sessfile -df grp1dirfile mc-sess using sess id file and search directory file |
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| ["othercommand1"], ["othercommand2"] | ["othercommand1"], ["othercommand2"] |
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| DougGreve | DougGreve |
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| FsFast, FsFastMotionCorrection, ["AFNI"] | FsFast, FsFastMotionCorrection, ["AFNI"] |
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| ## For example: ["Belliveau1991"] NameYear |
References/Cox1999 |
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| Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> | Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = Methods Description = {{{ The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/). }}} |
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| CategoryFsFastCommandsMotionCorrection | CategoryFsFastCommandsMotionCorrection |
Name
mc-sess - motion correction using ["AFNI"]
Synopsis
mc-sess -s [sessid] or -sf [sessidfile] -d [srchdir] or -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 |
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"]
Author
Links
FsFast, FsFastMotionCorrection, ["AFNI"]
References
References/Cox1999
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
Methods Description
The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/).