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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 '''Index''' <<TableOfContents>> |
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| {{{ mc-sess - motion correction using AFNI }}} |
mc-sess - MotionCorrection using [[AFNI]] |
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| {{{ mc-sess {-s [sessid] or -sf [sessidfile]} {-d [srchdir] or -df [srchdirfile]} [<options>] }}} |
mc-sess -s <sessid> -d <srchdir> [options] <<BR>> mc-sess -sf <sessidfile> -df <srchdirfile> [options] |
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| = Positional Arguments = {{{ None }}} |
= Arguments = == Positional Arguments == none |
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| = Required Flagged Arguments = {{{ -s [sessid] or -sf [sessidfile] description |
== Required Flagged Arguments == || -s <sessid> or -sf <sessidfile> || description || || -d <srchdir> or -df <srchdirfile> || description || |
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| -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 [stem] stem of output motion-corrected volume (fmc) -fmcstem [stem] 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 }}} |
== 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 || |
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| {{{ volume1 - description volume2 - description }}} |
|| outstem || motion-corrected volume || |
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| = Example 1 = {{{ |
= 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. = Examples = == Example 1 == |
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| }}} | |
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| = Example 2 = {{{ |
== Example 2 == |
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| }}} | = Bugs = none |
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| ["othercommand1"], ["othercommand2"] = Author = DougGreve |
[[othercommand1]], [[othercommand2]] |
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| FsFast, FsFastMotionCorrection, ["AFNI"] = References = References/Cox1999 = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> |
FsFast, FsFastMotionCorrect, [[AFNI]] |
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| = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFsFastCommandsMotionCorrection |
= References = [[References/Cox1999]] = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = Author = DougGreve |
Index
Contents
Name
mc-sess - MotionCorrection using AFNI
Synopsis
mc-sess -s <sessid> -d <srchdir> [options]
mc-sess -sf <sessidfile> -df <srchdirfile> [options]
Arguments
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.
Examples
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
Bugs
none
See Also
Links
FsFast, FsFastMotionCorrect, AFNI
Methods Description
The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/).
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>