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mc-sess - motion correction using ["AFNI"] mc-sess - MotionCorrection using ["AFNI"]
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mc-sess performs motion correction using the ["AFNI"] motion correction tool. By default, the motion correction 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.

Name

mc-sess - MotionCorrection 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

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"]

Author

DougGreve

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/).

Category

CategoryFsFastCommandsMotionCorrection

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