Hi,
For this kind of registration (EPI to structural) I would recommend using epi_reg, as this is what is was developed for. If you have fieldmaps (or blip-up-blip-down derived fieldmap images from topup) then this is likely to work even better.
If you've already tried epi_reg and want to try alternatives then let us know, as there are other options, but your flirt call is unlikely to work as you've chosen the EPI as the reference image and are using the default cost function of correlation ratio, and that does not tend to be a good combination, and also leaves you with the output having the same resolution as the EPI. In general we'd use the structural as the reference image, but I would definitely try epi_reg if you have not done this so far, as in my experience it works much better than any other option.
All the best,
Mark
> On 5 Nov 2018, at 18:29, Daniel Callow <[log in to unmask]> wrote:
>
> I am running flirt to try and align an anatomical T1w image to a bo image so that I can overlay FA and RGB scans on top to check them.
>
> However when I apply flirt with .....
>
> fslreorient2std /Volumes/DANIEL/${subj}/${subj}.${cond}/b0_brain_0.4
>
> flirt -dof 6 -in /Volumes/DANIEL/${subj}/${subj}.${cond}/anat_3d_final_al.nii -ref /Volumes/DANIEL/${subj}/${subj}.${cond}/b0_brain_0.4 -out /Volumes/DANIEL/${subj}/${subj}.${cond}/anat_registered_bo.nii
>
> my anat_registered_bo.nii file is not at all aligned with the b0_brain_0.4 image. In fact, it seems to have made the image blurrier, flipped it, and shifted it even further from the bo image in an affine manner. The flirt seems to have made the anatomical image. I don't know if screen shots are ever submitted or if they are how one would go about doing so, so I did not include any.
>
> Thank you for any help you might be able to provide in trouble shooting what I might be doing wrong.
>
> Best,
> Daniel Callow
>
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