Hi,
This isn't standard, but an easy thing to do is to modify the file:
$FSLDIR/bin/first_flirt
Just find the line:
echo "initial registration $doCortAlignment"
and on the line following this (the flirt call) add the following to the
end of the line:
-searchrx -180 180 -searchry -180 180 -searchrz -180 180
This will then do what you want.
If you don't want to modify everyone's copy of FSL (if you share it)
then you can
take a local copy of this script ($FSLDIR/bin/first_flirt), modify your
version and
run it from your own directory. Make sure you explicitly tell it which
version (using
the full path) as otherwise you might get the one in $FSLDIR/bin when
you don't
want it.
All the best,
Mark
Jennifer Addicks wrote:
> Hello,
> I am attempting to do subcortical segmentation using FIRST however I
> am having difficulties at the first stage of processing- registration.
> Using the -d flag I see that registration fails at the first step and
> I believe my images are incorrectly oriented relative to the MNI 152
> T1 template. Using the FLIRT linear registration GUI to register my
> images to the template I have noticed that using the advanced options-
> where one can select search angles for each axis ranging from -180 to
> 180, my registrations are successful. Therefore my questions are as
> follows:
> 1) Can anyone tell me how to add this angular range over which the
> registration occurs into the first_flirt script?
> I am reluctant to use the GUI and then the regular first_flirt script
> since the GUI and script register images to the linear and nonlinear
> MNI templates respectively.
>
> Thank you,
>
> Jennifer Phillips BSc, MSc (Cand.)
> Graduate Student
> Department of Neuroscience, University of Ottawa
> Mood Disorders Research Unit, University of Ottawa Institute of Mental
> Health Research
> 1145 Carling Ave, Research Tower, Room 6412
> Ottawa, Ontario K1Z 7K4
> Tel: 613.722.6521 x.6188
> Fax: 613.798.2982
> [log in to unmask] <mailto:[log in to unmask]>
> www.imhr.ca <http://www.imhr.ca>
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