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[[TableOfContents]] <<TableOfContents>>
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mc-sess - MotionCorrection using ["AFNI"] mc-sess - MotionCorrection using [[AFNI]]
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mc-sess -s <sessid> -d <srchdir> [options] [[BR]] mc-sess -s <sessid> -d <srchdir> [options] <<BR>>
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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. 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.
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["othercommand1"], ["othercommand2"] [[othercommand1]], [[othercommand2]]
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FsFast, FsFastMotionCorrect, ["AFNI"] FsFast, FsFastMotionCorrect, [[AFNI]]
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["References/Cox1999"] [[References/Cox1999]]

Index

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

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>

Author

DougGreve

mc-sess (last edited 2008-04-29 11:46:19 by localhost)