Hi, I have run into the same problem. I have managed to partially diagnose it, got some workarounds, but no real solutions. I would greatly appreciate FreeSurfer team for some feedback.
So it's all about orientations. FreeSurfer internally uses LPI and FSL (Especially FSLView) uses RAS. Try converting orig or brain mgz from mri folder of your FreeSurfer preprocessed subejcts into nifti using mri_convert (without any extra options). In FSLView they will look rotated as in your screenshot. When BBRegister runs the registration it creates not only transformation form EPI to T1 but also from RAS to LPI orientation. This is why your output images look rotated (but they are aligned with the output of the mgz to nifti conversion mentioned above). The workaround is to run fslreorient2std on the registered volumes. This will fix the apparent rotation visible in FSLView. However, in my case this translation matrix is one of many I am trying to combine. At the moment I need to apply a transformation, resample to do the LPI->RAS conversion and apply another transformation and resample again. I was wondering (here are the questions to FreeSurfer team): 1. Is my description of the problem accurate? 2. Is there a way to force BBRegister to output its transformation matrix having RAS space as a target? 3. Is there a way to apply some kind of a fix (LPI->RAS) to the transformation matrix? Best, Chris On 6 September 2011 23:23, noam Schneck <noam.schn...@gmail.com> wrote: > Dear FS experts, > > I'm sorry to pester but I am still having trouble trying to integrate > registration matrices produced by BBR into my FSL processing stream. I ran > BBR on a subject that I had run Recon-all for. I used BBR to register the > example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat. > I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the > example_func.nii.gz onto a T1 image that had been created by converting > bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this > time converting the orig.mgz to niftii. In both cases the example_func in T1 > space image produced by ApplyXFM is rotated about 90 degrees and also > inverted. I've attached a screenchot from fslview. >> >> > Thank you for your help, > Noam > > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
