Hello Mark,

The image I am starting with is actually already registered to the individual's structural image as a part of the preprocessing but is still in native space (i.e. the T1 wasn't aligned to MNI space prior to this registration). I thought after registering the EPIs to the subjects T1 I could then register the output to MNI.

To be clear you're saying that I should register the T1 to MNI first then register the EPI to the T1 in MNI space?

Thank you.

Kate

On Thu, Nov 3, 2016 at 5:04 PM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

You need to use epi_reg to register the functional (EPI) image from one subject to a structural image of that same individual. You cannot go directly to the standard (MNI) space.

So try it with the t1 and t1brain being that subject's structural (T1) scans and you should get a much better result. If you want to get to the standard space then you need to also register the structural to the standard space (with fnirt) and then combine the results.

All the best,

Mark

On 2 Nov 2016, at 22:50, Katherine Damme <[log in to unmask]> wrote:

The command that I ran is epi_reg --epi=<EPI image in native space after preprocessinf> --t1=MNI152_T1_3mm.nii.gz --t1brain=MNI152_T1_3mm_brain.nii.gz --out=<output name>

I don't see anything in the command line options to specify the registration parameters.

The related segmentation looked well aligned with the MNI template.

On Wed, Nov 2, 2016 at 3:07 AM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

That registration does look bad - in fact the EPI looks too small in general.
Are you using 6 DOF?
Have you checked the segmentation of the structural image? If that is not good then you can easily get problems.
Also, what does a registration without BBR (just using plain flirt with 6 dof) look like?
That might be useful to compare against.
If you are still stuck then let us know and it would be helpful to see the result as the registered EPI result in grayscale with the wmedge image overlaid in red.

All the best,
Mark

> On 1 Nov 2016, at 22:31, Katherine Damme <[log in to unmask]> wrote:
>
> Hello Everyone!
>
> Has anyone else had an issue with BBR putting the cerebellum in the occipital lobe when the participant's head is tipped forward?
>
> Any advice on how to fix this registration issue?
>
> Thank you.
>
> Kate Damme

> <epi_reg_cerebellum_err.png>