|
Size: 1555
Comment:
|
Size: 2094
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| ## 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 '''Index''' [[TableOfContents]] |
| Line 3: | Line 11: |
| {{{ mc-sess - motion correction using AFNI }}} |
mc-sess - MotionCorrection using ["AFNI"] |
| Line 7: | Line 14: |
| {{{ 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] |
| Line 11: | Line 17: |
| = Positional Arguments = {{{ None }}} |
= Arguments = == Positional Arguments == none |
| Line 16: | Line 21: |
| = Required Flagged Arguments = {{{ -sf [sessidfile] description |
== Required Flagged Arguments == || -s <sessid> or -sf <sessidfile> || description || || -d <srchdir> or -df <srchdirfile> || description || |
| Line 21: | Line 25: |
| -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 || |
| Line 60: | Line 36: |
| {{{ volume1 - description volume2 - description }}} |
|| outstem || motion-corrected volume || |
| Line 65: | Line 38: |
| = 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. |
| Line 70: | Line 41: |
| = 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 |
| Line 78: | Line 58: |
| = Author = DougGreve |
= Links = FsFast, FsFastMotionCorrect, ["AFNI"] |
| Line 81: | Line 61: |
| = Links = FsFast, FsFastMotionCorrection, ["AFNI"] |
= Methods Description = {{{ The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/). }}} |
| Line 85: | Line 67: |
| ## For example: ["Belliveau1991"] NameYear |
["References/Cox1999"] |
| Line 91: | Line 72: |
| = Methods Description = {{{ description description }}} = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFsFastCommandsMotionCorrection |
= Author = DougGreve |
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>