|
Size: 1031
Comment:
|
Size: 2135
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 |
| Line 3: | Line 8: |
| {{{ mc-sess - motion correction using AFNI }}} |
mc-sess - MotionCorrection using ["AFNI"] |
| Line 7: | Line 11: |
| {{{ mc-sess arg1 -i <arg2> -o <arg3> [<options>] }}} |
mc-sess -s [sessid] -d [srchdir] [<options>] [[BR]] mc-sess -sf [sessidfile] -df [srchdirfile] [<options>] |
| Line 12: | Line 15: |
| {{{ arg1 description }}} |
None |
| Line 18: | Line 18: |
| {{{ -i <arg2> description -o <arg3> description }}} |
|| -s [sessid] or -sf [sessidfile] || description || || -d [srchdir] or -df [srchdirfile] || description || |
| Line 27: | Line 22: |
| {{{ -f <fvalue> description description -g <gvalue> description description }}} |
|| -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 38: | Line 32: |
| {{{ volume1 - description volume2 - description }}} |
|| [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. |
| Line 44: | Line 38: |
| {{{ mc-sess foo -i f -o out }}} |
mc-sess -s grp1id -d grp1dir mc-sess using sess id and a search directory |
| Line 49: | Line 43: |
| {{{ mc-sess foo -i f -o out -f fvalue }}} |
mc-sess -sf grp1sessfile -df grp1dirfile mc-sess using sess id file and search directory file |
| Line 54: | Line 48: |
| ["othercommand1"], ["othercommand2"] | ["othercommand1"], ["othercommand2"] |
| Line 57: | Line 51: |
| DougGreve | DougGreve |
| Line 60: | Line 54: |
| FsFast, FsFastMotionCorrection, ["AFNI"] | FsFast, FsFastMotionCorrection, ["AFNI"] |
| Line 63: | Line 57: |
| ## For example: ["Belliveau1991"] NameYear |
References/Cox1999 |
| Line 67: | Line 60: |
| Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> | 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/). }}} |
| Line 71: | Line 69: |
| CategoryFsFastCommandsMotionCorrection | CategoryFsFastCommandsMotionCorrection |
Name
mc-sess - MotionCorrection using ["AFNI"]
Synopsis
mc-sess -s [sessid] -d [srchdir] [<options>] BR mc-sess -sf [sessidfile] -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 |
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.
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
See Also
["othercommand1"], ["othercommand2"]
Author
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/).