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Hi, What cost function are you using? Have you tried different ones? Also, do you start nearly aligned or in quite different orientations? All the best, Mark On 1 May 2009, at 16:50, John Kuster wrote: > Hello Hedok, > > Our slices are about 5mm thick, 3.5x3.5 voxes, for 16 slices, > partial > field, with no gap, but I have to check on the gap, it may be 1mm > because of constraints. > > Flirt basically worked well for most of our subjects, but failed > for a > few. Do you think the resolution differences combined with the partial > field may be putting flirt on the threshold of failing? I have tried > cleaning up the ASL scans by cropping the background using bet with > f=.2. This helped for a few, but not for the worst ones. Then, I > tried masking the original image and the result was similar with the > same few failing. > > I am basically at a loss as to how I can get flirt to work a little > better. > > thanks for your input! > > Jake > > >> Dear John, >> >> Just curious about your ASL(arterial spin labeling) image parameters. >> >> Do you acquire them with very thick slice(~7mm) with gap ~1mm?. >> Is this partial or full brain coverage? >> >> I don't have much experience in ASL, but I remember it was quite >> difficult to even coregister anatomical with perfusion weighted >> image. >> Let me know how it goes. >> >> Hedok >> >> Jesper Andersson wrote: >>> Dear John, >>> >>> just to add to Matt's previous comment. >>> >>>> I tried to run the following command, >>>> >>>> Command: >>>> fnirt --ref=swap_CTRL02_T1.nii.gz --in=swap_CTRL02_ASL.nii.gz >>>> --aff=CTRL02_ASL2T1_auto1.mat --cout=CTRL02_ASL2T1_auto2.mat >>> >>> From the names of your --ref and your --in file I am guessing you >>> are >>> trying to register a subjects ASL scan to the same subjects >>> T1-weighted structural scan. Is that correct? >>> >>> If so there are two issues: >>> 1. Since it is the same subject you really only need 6 dof, i.e. all >>> you need to do is to make sure the images are in the same >>> "position". >>> 2. The contrast in an ASL image is very different from that of a >>> T1-weighted image, something that fnirt would struggle with. >>> >>> Both these issues suggest that what you really need is flirt, and >>> that >>> will run just fine on a 32bit machine. >>> >>> Good luck Jesper >> >> >> >