Hi Mark,

I am using FSL 4.1.8. I have FSL 5 on another computer though. I will try things out there and let you know how it went.

Thanks, Maren


On Thu, Jun 6, 2013 at 12:39 PM, Mark Jenkinson <[log in to unmask]> wrote:
Dear Maren,

What version of FSL are you using?
In the recent versions there is a BBR option between 7 DOF and 12 DOF.
This is what we recommend using, and this is what I used to get a good registration.

All the best,
Mark


On 6 Jun 2013, at 14:57, Maren Strenziok <[log in to unmask]>
 wrote:

Hi Mark,

I started out with the default settings, then trying out different degrees of freedom and linear/non-linear registration. All came out equally bad. I am not sure what you mean by BBR? Can you please explain? My default settings are normal search with 6 DoF for the Main structural image and normal search with 12 DoF for the Standard Space. I will re-do the registration with these settings. Did you register to 1mm or 2mm standard space and got good results?

Maren 


On Wed, Jun 5, 2013 at 5:32 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

When I ran this registration with the default recommendations (BBR for example_func to highres, and 12 DOF + nonlinear for the highres to standard) I got very good registrations, which were a _lot_ better than the ones you sent.  Is there any reason you were not using the defaults?

All the best,
Mark



On 4 Jun 2013, at 14:45, Maren Strenziok <[log in to unmask]> wrote:

Hi Mark,

I uploaded those two images.

Thanks, Maren


On Mon, Jun 3, 2013 at 6:26 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

I'm afraid these files are not useful on their own.
I also need to see the example_func and highres images.

All the best,
Mark


On 3 Jun 2013, at 14:56, Maren Strenziok <[log in to unmask]> wrote:

Hi Mark,

the BET result looks fine. I just uploaded two nifti files, example_func2standard and example_func2highres. I put my first name in the name of the files so that you can easily find them on your server. Please let me know if you needed any additional files.

Best regards, Maren


On Thu, May 30, 2013 at 4:18 AM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

That does look bad to me.  Have you checked that the brain extractions are OK?
It is hard to diagnose anything without more information though.  Can you upload the relevant nifti images to this site:
then I'll have a look at them and hopefully figure out a way to improve the results.

All the best,
Mark


On 28 May 2013, at 15:39, Maren Strenziok <[log in to unmask]> wrote:

Hi,

I have trouble to judge the quality of a registration result. I registered an fMRI scan (acquired with 3x3x3 resolution, large field of view) to 1mm MNI standard space via a high resolution mprage (roughly 1x1x1 resolution). I used normal search, 12 DoF for the mprage and for the standard brain. I checked non-linear for the registration to standard space. The registration of the functional data to the standard brain (and also to the mprage) don't look good  (see attached image) compared to what I have seen before using another imaging program. Am I too picky or is there a way to get better results? Could the poor quality be related to an error message that I get when I load in the data? It says: Warning - have auto-set BET preprocessing option and/or registration DoF on the basis of image fields-of-view; check settings.

Maren
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