Hi Jeff,
as I said, I think changing tbss_2_reg behaviour should be your last resort as this would require quite a lot of tweaking... Try first creating your own 7T FA target to see if this helps.
For this, you'd need to run flirt manually on all your FA images (even better would be possibly on your MD or nodif images, as they offer a better contrast-to-noise ratio between the cortical grey matter and the background, and then apply the .mat to the corresponding FA images), average all the FA (same number of subjects per group if you have several groups) and copy this "target.nii.gz" in your TBSS directory. Finally, re-run tbss2 with the -t target.nii.gz option.
Cheers,
Gwenaelle
> De: Jeff Eriksen <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] bad registration TBSS with 7T DTI 25 slices 1.7 mm
> À: [log in to unmask]
> Date: Mercredi 23 mars 2011, 22h16
> Thank you for your suggestions. I
> will play around with BET some more, and perhaps try a
> manual edit as well. Regarding changing the default
> tbss_2_reg behavior, I should have also asked "how". I am a
> newbie to Linux and shells, and do not know where to begin.
>
> -Jeff
--------------------------------------------------------------------
Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
--------------------------------------------------------------------
|