Aha, I didn't even know that mcflirt had this option. MJ may correct
me, but I doubt this option has had huge amounts of testing so it
might be safer to use eddy_correct (you may want to change the flirt
option in there to use dof 9 instead of 12).
If you want to change the options to mcflirt call in FEAT that's very
easy, but you would need to edit the scripts as it's not settable in
the GUI.
Just edit $FSLDIR/tcl/featlib.tcl and search for the first mention of
"mcflirt"
Cheers.
On 26 Aug 2007, at 09:20, Jack Grinband wrote:
> Hi Steve,
>
>> Hi - the DOF are not controllable in mcflirt as it always uses rigid
>> body correction (dof=6) and is tuned for that.
>
> I'm not sure I understand. When I run mcflirt with -dof 9, I get
> better
> results than the default -dof 6. I was just hoping to find where
> this value
> is set in feat so I don't have to rewrite all my scripts. But it
> sounds
> like you're saying that since the upgrade, this value can no longer be
> modified. Is that right? thanks,
>
> jack
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
|