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| ## see dtrecon as an exmaple | ## See HelpOnCommandTemplate for description of formatting ## ## Note: If you are modifying this page please refer to the ## CommandTemplate page and confirm that this page has the latest ## CommandTemplate formatting [[Navigation(children)]] '''Index''' [[TableOfContents]] |
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| {{{ mc-sess - motion correction using AFNI }}} |
mc-sess - MotionCorrection using ["AFNI"] |
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| {{{ mc-sess -sf [sessidfile] -df [srchdirfile] -s [sessid] -d [srchdir] [<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 = {{{ -sf [sessidfile] description |
== Required Flagged Arguments == || -s sessid or -sf sessidfile || description || || -d srchdir or -df srchdirfile || description || |
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| -df [srchdirfile] description -s [sessid] description -d [srchdir] 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 [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 }}} |
== 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 || |
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| {{{ volume1 - description volume2 - description }}} |
|| outstem || motion-corrected volume || |
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| = Example 1 = {{{ mc-sess -i f -o out }}} |
= 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. |
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| = Example 2 = {{{ mc-sess -i f -o out -f fvalue }}} |
= 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 |
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| = Author = DougGreve |
= Links = FsFast, FsFastMotionCorrect, ["AFNI"] |
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| = Links = FsFast, FsFastMotionCorrection, ["AFNI"] |
= Methods Description = {{{ The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/). }}} |
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| ## For example: ["Belliveau1991"] NameYear |
["References/Cox1999"] |
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| = Methods Description = {{{ description description }}} |
= Author = DougGreve |
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| = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFsFastCommandsMotionCorrection |
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>