Hi Satra et al,

thanks a lot and it would be great if you could find some code!

In the meantime, I tried the following based on information from Kiho Im:

# we have to first remove transformation of 'vertex to RAS' embedded in smoothwm surface.
mris_transform lh.smoothwm identity.xfm ./lh.smoothwm.clean

# then use the flirt T1-to-b0 matrix converted from .mat to .xfm format to transform the surface
mris_transform lh.smoothwm.clean T1-to-b0.xfm lh.b0.smoothwm

And of course: it didn't work.. In the attached screenshot, the red surface is the original one which kind of fits the b0 image but not very well (it obviously fits the original T1 very well). The blue is the transformed surface (lh.b0.smoothwm) and is completely off.

Inline image 1

Do you know what I could be doing wrong? I also attached both tranforms. Maybe I just converted them wrong.

Thanks!!
Daniel


On Thu, Apr 11, 2013 at 10:53 AM, Satrajit Ghosh <satra@mit.edu> wrote:
hi dan,

if you use bbregister to match the DTI b0 to freesurfer space, then you can transform the surface back (no guarantees on the tesselations though i think). the only additional component here would be a tkr transform that's based on the conformed space. i might even have some python code lying around to do this. i'll take a look.

cheers,

satra

On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn <daniel.haehn@childrens.harvard.edu> wrote:
Hi all,

I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space.

I found http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but this describes transforming the B0 to T1 space and then match the surfaces. I don't want to change the DTI B0 image.

 What is the best way to do that? 

Thank you very much!
Daniel

--
Daniel Haehn
FNNDSC / BCH
+1.857.218.5140

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Daniel Haehn
FNNDSC / BCH
+1.857.218.5140