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
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.