what do you mean that it is in the wrong orientation? It should be in the same orientation as the anatomical. How does the reg look in tkregister2? Note that fslview can display volumes in odd orientations even when the orientation is correct. doug

On 04/13/2012 03:31 AM, Erlend Hodneland wrote:

Hi,

we are trying to register fmri FEAT data (example_func.nii) to the anatomical scan (processed in Freesurfer) using bbregister to opt. the affine registration before running FNIRT.

However, the orientation of the registered image is flipped around and is incorrect after applying bbregister.

We have tried:

1. bbregister --s subj_501 --mov example_func.nii.gz --reg

register.dat --init-header --bold --o example_func2highres-fs.nii 2) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-fsl --bold --o example_func2highres-fs.nii 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat "myfeatdirectory" 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat (this one looks correct) followed by bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-reg tkreg.dat --bold --o example_func2highres-fs.nii

5. reorienting to match the highres:

   fslorient -swaporient example_func fslswapdim example_func x -y z example_func_swap (correct

orientation)

followed by bbregister --s subj_501 --mov example_func_swap.nii.gz --reg register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii

with the output being flipped in wrong orientation for all options.

We would greatly appreciate if you have any suggestions for how to overcome this problem!

Cheers/Sincerly/All best

Erlend Hodneland

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