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Hi Mark, Thanks for your reply. I do not have fieldmaps for these scans. They're from a spiral-in SENSE sequence, which seems to help with the ventral frontal distortions, but it doesn't fix all distortions. I took a closer look at highres.nii.gz and example_func2highres.nii.gz, and they are generally aligned using 6 DOFs. However, the alignment probably isn't perfect, and I can see that the edges (particularly around DLPFC) aren't matched up: the functional data is compressed/distorted relative to the highres. Since I don't have fieldmaps for this particular dataset, what are my options (assuming I have some)? Will masking the example_func better help? It seems to have some excess non-brain material, even after BET. Will an unsmoothed example_func help? These were originally smoothed with a 6mm kernel since I made the example func from my preprocessed data. Thanks! David On Jul 12, 2011, at 12:32 PM, Mark Jenkinson wrote: > 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/ >> >> >> >> >> >>