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mc-sess -s sessid -d srchdir [<options>] [[BR]] mc-sess -sf sessidfile -df srchdirfile [<options>] |
mc-sess -s sessid -d srchdir [options] [[BR]] mc-sess -sf sessidfile -df srchdirfile [options] |
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|| -s sessid or -sf sessidfile || description || || -d srchdir or -df srchdirfile || description || |
|| -s <sessid> or -sf <sessidfile> || description || || -d <srchdir> or -df <srchdirfile> || description || |
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|| -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 || |
|| -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 || |
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| || -rlf runlistfile || only process those in the runlist file || | || -rlf <runlistfile> || only process those in the runlist file || |
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Index TableOfContents
Name
mc-sess - MotionCorrection using ["AFNI"]
Synopsis
mc-sess -s sessid -d srchdir [options] BR 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
["othercommand1"], ["othercommand2"]
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
["References/Cox1999"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>