## 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''' <> = Name = mri_motion_correct2 - averages a number of volumes and performs MotionCorrection (reincarnate of [[mri_motion_correct]]) = Synopsis = mri_motion_correct -o outvol -i invol1 -i invol2 [] = Arguments = == Positional Arguments == || outvol || description || || invol1 || description || || invol2 || description || == Required Flagged Arguments == -o outvol -i invol1 -i invol2 == Optional Flagged Arguments == ||-wild || assume unmatched args are input files || ||-tmpdir tmpdir || directory for temporary files || ||-nocleanup || do not delete temporary files || ||-umask umask || set unix file permission mask || ||-cm || COR volumes conform to min voxel size || ||-version || print version and exit || ||-debug || print lots of stuff to screen || = Outputs = || outvol || averaged and motion corrected volume || = Description = description = Examples = == Example 1 == mri_motion_correct2 -o ../orig -i 002 -i 003 motion correct and average the 2 COR volumes and output to a COR volume in ../orig == Example 2 == mri_motion_correct2 -cm -i 001.mgz -i 002.mgz -i 003.mgz -o ../orig.mgz motion correct and average the 3 .mgz volumes, conform to min voxel size, and output to ../orig.mgz = Bugs = None = See Also = [[mri_motion_correct]], [[mri_info]], [[mri_convert]], [[minctracc]], [[mincresample]], [[mincaverage]] = Links = FreeSurfer = Methods Description = {{{ ?? }}} = References = [[References/Lastname###]] = Reporting Bugs = Report bugs to = Author/s = DougGreve