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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: >>>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C >>>> 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 >>>> <Doc1.docx> >>>> >>>> >>>> >>> >>> >> >> > >