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'''Index'''
<<TableOfContents>>


= Name =
mri_motion_correct.fsl - Aligns and averages two or more volumes. Uses the FSL flirt program.

= Synopsis =
The inputs and output can be any format accepted by [[mri_convert]]

= Description =
calls fsl_rigid_register which calls flirt. See fsl_rigid_register -help. This should basically do the same thing as mri_motion_correct and mri_motion_correct2. One difference is that mri_motion_correct.fsl forces the input data to be float when converting to ANALYZE, and so the final output is is also float. mri_motion_correct2 keeps the native precision.

= Examples =
== Example 1 ==
{{{
mri_motion_correct.fsl -i 002.mgz  -i 003 -o mc4.img
}}}
002.mgz is a volume in compressed MGH format.
003 is in COR format.
mc4.img (the output) is in analyze format.

== Example 2 ==
Say you have many input volumes, eg, 001.mgh ... 010.mgh, and 
you do not want to list all of them on the command-line with
a -i. Then you can:
{{{
mri_motion_correct.fsl -o mc.mgh  -wild *.mgh
}}}
Note that -wild must appear BEFORE the wildcard.

= See Also =
[[mri_motion_correct]]

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>