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Name

mc-sess - motion correction 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

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

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/).

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##

## Note: If you are modifying this page please refer to the

## CommandTemplate page and confirm that this page has the latest

## CommandTemplate formatting
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-{{{
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-}}}
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-{{{

mc-sess -s [sessid] or -sf [sessidfile] -d [srchdir] or -df [srchdirfile]  [<options>]

}}}
+mc-sess -s [sessid] or -sf [sessidfile] -d [srchdir] or -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 [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

}}}
+|| -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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