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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 > > >