Hi Javier,
That looks fine - if your results don’t look good you might need to do some parameter tuning for FNIRT as your resolution and brain size are quite different from what that configuration file was made for.
Regarding the resampling issue: most FSL tools do as much of the analysis as possible in the native resolution images and resample only in order to do the group stats. Trilinear interpolation should normally be fine - you will get blurring even with nearest neighbour as the registered voxel grids of different scans won’t line up once they have been registered to the template.
It’s difficult to make very concrete recommendations without knowing what analysis you intend to run; if you are going to use FEAT for the fMRI analysis, that should do all the registration steps for you (although it might need some tweaking, as it is mostly designed for human data).
Hope that helps and let us know if you have any more questions!
Cheers,
Eelke
> On 27 Jun 2015, at 10:07, Javier Sanz Perez <[log in to unmask]> wrote:
>
> Hi Eelke,
>
> Sorry for responding so late. That helped, thank you very much! Now I plan to use FNIRT and do something similar to the FNIRT example:
>
> Registering functional data (or any non-T1 image data) to MNI152 (via structural scan)
>
> bet my_structural my_betted_structural
> flirt -ref my_betted_structural -in my_functional -dof 6 -omat func2struct.mat
> flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat
> fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
> applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_functional --warp=my_nonlinear_transf --premat=func2struct.mat --out=my_warped_functional
>
>
> Since my images have less than 20 slices and the template has more than 100 slices, I'm worried about so much interpolation (by the way, in order to not alter the results is it recommended trilinear or nearest neighbour?). Is there a way to register my anatomic and functional images to the template and obtain an output image with the same FOV and voxel size of my images?I know the FOV and voxel size is taken from the reference, but I think it should be a way (inverse transformation, applywarp, invwarp ...).
>
>
>
> Thank you very much,
>
> Javier
>
>
>
>
> 2015-06-22 18:25 GMT+02:00 Eelke Visser <[log in to unmask]>:
> Hi Javier,
>
> Sorry for not responding earlier - I was away for a few days. As your image appears to be quite inhomogeneous, running it through fast (with -B -t 2 options) to remove the bias field might improve things. The bias corrected output from fast is called <input image>_restore.
>
> If that doesn’t help, some screenshots with the crosshair in the same location for both images would help me to see where the registration errors are.
>
> Cheers,
> Eelke
>
> > On 19 Jun 2015, at 05:35, Javier Sanz Perez <[log in to unmask]> wrote:
> >
> > Hi Eelke,
> >
> > Sorry, you are right, it's hard to see. I attach two screenshots more. I rewrote the header of the anatomic images to multiply the spatial resolution by 10, in order to improve the results of BET and other tools. The template remained untouched.
> >
> > Thanks for your help,
> > Regards,
> >
> > Javier
> >
> > 2015-06-18 23:36 GMT+02:00 Eelke Visser <[log in to unmask]>:
> > Hi Javier,
> >
> > I still find it a bit hard to see what is going on as your scan is behind the atlas image. Would you mind adding a screenshot with the actual scan on top?
> >
> > Thanks,
> > Eelke
> >
> >
> >
> >> On 17 Jun 2015, at 23:19, Javier Sanz Perez <[log in to unmask]> wrote:
> >>
> >> Hi Eelke,
> >>
> >> Thank you for your answer. I ran flirt -in ${anatomic_dir}/anatomic_brain.nii.gz -ref ${template} -dof 6 -out ${anatomic_dir}/anatomic_tostandard.nii.gz -omat ${anatomic_dir}/anatomic_tostandard_transform.mat.
> >> I attach two screenshots: one with 6 degrees of freedom and the other with 12 degrees of freedom.
> >>
> >> Best regards,
> >>
> >> Javier
> >>
> >>
> >> 2015-06-18 3:27 GMT+02:00 Eelke Visser <[log in to unmask]>:
> >> Hi Javier,
> >>
> >> The anisotropy is not necessarily a problem for FLIRT, but it is a bit hard to guess what is going on without seeing the images. Would it be possible to share some screenshots along with the options you used when running it?
> >>
> >> Cheers,
> >> Eelke
> >>
> >>
> >>> On 17 Jun 2015, at 10:48, Javier Sanz Perez <[log in to unmask]> wrote:
> >>>
> >>> Hi everyone,
> >>>
> >>>
> >>>
> >>> I’m having problems trying to register anisotropic anatomic rat images (0.2x0.2x1 mm3) to an isotropic template (1.25x1.25x1.25 mm3) with FLIRT, 6 and 12 DoF. The resulting image is not properly registered to the template.
> >>>
> >>>
> >>>
> >>> I was wondering if the problem was due to the high anisotropy of the images (1/0.2=5) compared to the isotropy of the template. How can the registration improve?
> >>>
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> All the best,
> >>>
> >>>
> >>>
> >>> Javier
> >>>
> >>
> >>
> >> <FLIRT_6dof.png><FLIRT_12dof.png>
> >
> >
> > <6dof_template_behind.png><12dof_template_behind.png>
>
>
