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[[Navigation(children)]]
'''Index'''
[[TableOfContents]]
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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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= Positional Arguments =
None
= Arguments =
=
= Positional Arguments ==
none
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= Required Flagged Arguments =
|| -s [sessid] or -sf [sessidfile] || description ||
|| -d [srchdir] or -df [srchdirfile] || description ||
== Required Flagged Arguments ==
|| -s sessid or -sf sessidfile || description ||
|| -d srchdir or -df srchdirfile || description ||
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= 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] ||
== 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 ||
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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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|| [outstem] || motion-corrected volume || || outstem || motion-corrected volume ||
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= Example 1 = = Examples =
=
= Example 1 ==
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= Example 2 = == Example 2 ==
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= Bugs =
none

Navigation(children) 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>

Author

DougGreve

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