Differences between revisions 16 and 26 (spanning 10 versions)
⇤ ← Revision 16 as of 2004-08-10 13:26:37 →
Size: 2113
Editor: DavidTuch
Comment: wikified MotionCorrection
← Revision 26 as of 2008-04-29 11:46:19 → ⇥
Size: 2094
Editor: localhost
Comment: converted to 1.6 markup
Deletions are marked like this. Additions are marked like this.
Line 7: Line 7:
'''Index'''
<<TableOfContents>>
Line 8: Line 11:
mc-sess - MotionCorrection using ["AFNI"] mc-sess - MotionCorrection using [[AFNI]]
Line 11: Line 14:
mc-sess -s [sessid] or -sf [sessidfile] -d [srchdir] or -df [srchdirfile] [<options>] mc-sess -s <sessid> -d <srchdir> [options] <<BR>>
mc-sess -sf <sessidfile> -df <srchdirfile> [options]
Line 13: Line 17:
= Positional Arguments =
None		 = Arguments =
== Positional Arguments ==
none
Line 16: Line 21:
= 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 ||
Line 20: Line 25:
= 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 ||
Line 28: Line 33:
|| -rlf [runlistfile] || only process those in the [runlist] file || || -rlf <runlistfile> || only process those in the runlist file ||
Line 31: Line 36:
|| [outstem] || motion-corrected volume || || outstem || motion-corrected volume ||
Line 34: Line 39:
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.
Line 36: Line 41:
= Example 1 = = Examples =
== Example 1 ==
Line 41: Line 47:
= Example 2 = == Example 2 ==
Line 46: Line 52:
= Bugs =
none
Line 47: Line 56:
["othercommand1"], ["othercommand2"]

= Author =
DougGreve		 [[othercommand1]], [[othercommand2]]
Line 53: Line 59:
FsFast, FsFastMotionCorrection, ["AFNI"]

= References =
References/Cox1999

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>		 FsFast, FsFastMotionCorrect, [[AFNI]]
Line 66: Line 66:
= Category =
## For example: CategoryFreeSurferCommandVolumeConversion
CategoryFsFastCommandsMotionCorrection		 = References =
[[References/Cox1999]]

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author =
DougGreve

Index

Contents

  1. Name
  2. Synopsis
  3. Arguments
    1. Positional Arguments
    2. Required Flagged Arguments
    3. Optional Flagged Arguments
  4. Outputs
  5. Description
  6. Examples
    1. Example 1
    2. Example 2
  7. Bugs
  8. See Also
  9. Links
  10. Methods Description
  11. References
  12. Reporting Bugs
  13. Author

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)