|
Size: 1031
Comment:
|
Size: 2096
Comment: fixed typo
|
| 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 [[Navigation(children)]] '''Index''' [[TableOfContents]] |
| Line 3: | Line 12: |
| 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 = |
|
| Line 4: | Line 64: |
| mc-sess - motion correction using AFNI }}} = Synopsis = {{{ mc-sess arg1 -i <arg2> -o <arg3> [<options>] |
The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/). |
| Line 11: | Line 67: |
| = Positional Arguments = {{{ arg1 description }}} |
= References = ["References/Cox1999"] |
| Line 17: | Line 70: |
| = Required Flagged Arguments = {{{ -i <arg2> description -o <arg3> description }}} = Optional Flagged Arguments = {{{ -f <fvalue> description description -g <gvalue> description description }}} = Outputs = {{{ volume1 - description volume2 - description }}} = Example 1 = {{{ mc-sess foo -i f -o out }}} = Example 2 = {{{ mc-sess foo -i f -o out -f fvalue }}} = See Also = ["othercommand1"], ["othercommand2"] |
= Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> |
| Line 57: | Line 74: |
| DougGreve | DougGreve |
| Line 59: | Line 76: |
| = Links = FsFast, FsFastMotionCorrection, ["AFNI"] = References = ## For example: ["Belliveau1991"] NameYear = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = 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>