Index

Name

command - 1/2 sentence summary

Synopsis

command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4]

Arguments

Positional Arguments

argA

brief description

detailed description (eg, help file information)

argB

brief description

detailed description (eg, help file information)

Required Flagged Arguments

--s subject

FreeSurfer subject name

--mov volid

input/movable volume

--reg register.dat

output registration file

Optional Flagged Arguments

--nolog

no log file

using this flag will not create a log file

-flag4 arg4

brief description

detailed description (eg, help file information)

Outputs

volume1

description

volume2

description

Description

type bbregister --help to get the full help on this.

Examples

Example 1

Intialize with FLIRT, view result with tkregister2:

Example 2

Intialize with SPM, view result with tkregister2:

== Example 3 ==

Register a partial FoV using whole FoV as intermdediate:

Tips

When the registration fails, it could be because of a bad initialization. Check the first value in the mincost file. It will be at a value between 0 and 1.1, with 0 being perfect. Look at your good subjects to get an idea of what range to expect for your well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that.

Bugs

None

See Also

othercommand1, othercommand2

Links

FreeSurfer, FsFast

Methods Description

description
description

References

References/Lastname###

Reporting Bugs

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

Author/s

JaneSmith

bbregister (last edited 2011-10-17 12:48:46 by KhoaNguyen)