Hi,
You need to make sure that you're not getting confused by the mixing
of the different software versions and -t vs -T options. I'm not sure
which of these options you're concentrating on getting to work.....
Is the data in the right general orientation (wrt MNI standard space
images)? If not it's probably worth using fslswapdim to get them
oriented.
Given that this is a pediatric population I would stick with the -n
option probably?
Cheers.
On 23 Apr 2008, at 20:25, Conrad Rockel wrote:
> Hi,
>
> I've been searching through the forum, trying to figure out why my
> target
> ends up in a weird oblique position when rotated to MNI space.
>
> Because I work with a pediatric population, I have been using the '-t'
> option, though now running with '-T' to see if that works any better.
>
> My RL,AP, and SI seem appropriate. Furthermore, despite the bizarre
> final
> position, the all_FA images seem in line with each other, it is just
> this
> last step of target to MNI that seems to be mucked up.
>
> I have recently upgraded to 4.04 from 3.39, and never seemed to have
> this
> problem in the old version. I should note that I am using a target
> image
> I've never used before.
>
> Since the registration of my entire dataset takes so long, do you
> think I
> should flirt some potential targets to MNI before running
> tbss_2_reg? Can
> you think of what this may be due to?
>
> Cheers,
>
> Conrad
>
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