Hi David,
Did you have fieldmaps for these EPI scans?
I suspect that the problem is actually in your example_func2highres
scan and made slightly more prominent in the standard space. The
areas which don't match well look like the result of EPI distortion to
me. You highres2standard looks great, so that means that it really
isn't FNIRT that is the problem. There's a limit to how well I can really
tell from the images for the example_func2highres as the edges are
always rather poorly estimated, but have a close look in FSLView and
see if in fact the DLPFC is well aligned in these or not.
All the best,
Mark
On 12 Jul 2011, at 17:19, David V. Smith wrote:
> Hello,
>
> I'm trying to improve my FNIRT registration (example_func2standard); however, I'm not sure where to begin because (I think) my highres2standard looks fairly reasonable (both for FNIRT and FLIRT):
> http://www.duke.edu/~dvs3/highres2standard_FLIRT.png
> http://www.duke.edu/~dvs3/highres2standard_FNIRT.png
>
> Nevertheless, for the FNIRT version of example_func2standard, you can see that FNIRT is shrinking DLPFC a little too much in the example_func2standard, especially when you compare this to the FLIRT version.
> http://www.duke.edu/~dvs3/example_func2standard_FLIRT.png
> http://www.duke.edu/~dvs3/example_func2standard_FNIRT.png #note misaligned DLPFC here
>
> (The example_func2highres also looks fine.)
> http://www.duke.edu/~dvs3/example_func2highres.png
>
> You can see my commands here: http://www.duke.edu/~dvs3/example_reg.sh (sorry, attachment was rejected). I think I really only have three (minor) deviations from the defaults:
> 1) using sinc interpolation: -interp sinc -sincwindow hanning
> 2) using the header: -usesqform
> 3) using our own study-specific template from ANTs and FLIRTed to MNI. I don't think this is a problem, but you can inspect the images, if you like:
> http://www.duke.edu/~dvs3/MNI_diffeo.nii.gz
> http://www.duke.edu/~dvs3/MNI_diffeo_brain.nii.gz
>
> Anyway, I've already tried a couple of things on the FNIRT documentation (e.g., adjusting the standard_mask size, specifically making it smaller; and applying the mask only in the final iterations: --applyrefmask=0,0,0,0,1,1), but nothing really preserves the shape of DLPFC (or really even makes a noticeable difference in the output). Is there anything else I could try? Or is this something I shouldn't even worry about?
>
> Thanks!
> David
>
> --
> David V. Smith
> Graduate Student, Huettel Lab
> Department of Psychology and Neuroscience
> Duke University
> Durham, NC 27708
> http://www.mind.duke.edu/huettellab/
>
>
>
>
>
>
|