On Wed, Oct 12, 2011 at 6:45 AM, Saad Jbabdi <[log in to unmask]> wrote:

Hi Monica

I would suggest that you start by calculating the following transforms: DTI <-> T1 <-> PD

Then depending on which space you want to analyse your tractography results in, you can simply give probtrackx the transformation MySpace->DTI

For example, if you want your results in the individual T1 space, you can transform your LGN mask from PD to T1 space, then run probtrackx using T1->DTI
If you want to store all your results in standard space, you need to additionally calculate T1<->MNI, concatenate this transform with the DTI<->T1 (using convert_xfm or convertwarp), then use MNI->DTI within probtrackx.

Saad

On 11 Oct 2011, at 22:11, Monica Giraldo wrote:

> Hello, I have a proton density image that I am using to define the LGN, the DTI and a T1. I need to trace the tractography between my LGN to the rest of the brain, to see how is this area connected with other areas. The problem is that each of my three images are in different spaces. The T1 can be corregistered to the DTI and proton density with no problem, but if I take the DTI to the proton density my tensors will be damage, and if I take the porton density to the DTI space then I won't be able to see the LGN.
>
> So, what I am doing right now is drawing the LGN over the proton density image and adding them, and then taking this new image to the DTI space. This way Im able to create my LGN mask and do the tractography with all the images in the DTI space... but would be a lot easier it I could take the DTI to the proton density space, also because my region would be more exact (since the proton density has better resolution), is it possible to apply some correction or use other images apart from the DTI to do the tractography?
>
> Thanks,
>

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad