Hi Gaby, I re-ran your registration and it worked fine. However, I did get the brain in the corner of the image on the old non-patched version, because of the bug for small voxels (one or more dims less than 0.5mm). So it looks like your site hasn't applied the patch that we sent out a couple of months ago. If you do this then I think the registrations should be fine. Re patches: take the appropriate small patch file from http://www.fmrib.ox.ac.uk/fsldownloads/patches/3.2 and then: cd $FSLDIR/.. gunzip [your downloaded patch file] tar xvf [the uncompressed patch file] All the best, Mark On 17 Dec 2004, at 07:36, Gaby Pell wrote: > Hi Mark, > > Thanks for your response on this matter. I am still having problems > with > the registration task, as follows. I am simply trying to register the > large FOV scan to the standard space template and am finding that the > registration leaves the brain lodged in the bottom left corner. > However, > the fix you suggest in the FSL FAQ of shifting it with the translation > matrices does not seem to do the trick. > > Interestingly, a registration with the FSL3.1 version of flirt works > fine > in this case. > > Thanks, > > Gaby > > On Thu, 9 Dec 2004 16:08:38 +0000, Mark Jenkinson <[log in to unmask]> > wrote: > >> Hi Gaby, >> >> The origin, as far as Flirt is concerned, is always in the >> corner, however Fslview and other programs will report >> standard space coordinates for images when the appropriate >> sform (for nifti) or origin (for analyze) is set. Therefore >> you can't go by what they report. >> >> As for getting the COV shift correct, the offsets you >> calculate seem fine - the only question is which transform >> are you adding them to? The answer to this depends on >> what you are doing and why. For instance, if you wanted >> to create a larger FOV for the output image which had the >> same coordinate system as the reference, but with some >> "padding" around the edges, and then keep the COV of the >> enlarged output at the same point in the object as the >> COV of the reference image, then adding this shift to the >> input->reference transformation would be the right thing >> to do. However, if you wanted the output volume to be >> different, say in the coordinate system of the input volume, >> but somehow reoriented and with a new FOV then you'd need >> something else. I guess that, except for having some padding >> around the reference space of the standard brain, I'm not >> sure what you would want to do. If this is what you want to >> do then I think the following should work: >> flirt -in invol -ref avg152T1_brain -omat in2avg.mtx >> emacs in2avg.mtx (and add the offsets to the last column) >> flirt -in invol -ref bigrefvol -applyxfm -init in2avg.mtx -out >> in2big >> >> If bigrefvol is 250x196x250mm then this should do what you want. >> If it doesn't, let me know exactly what you've done and what >> went wrong. >> >> All the best, >> Mark >> >> P.S. An alternative to editing the matrix file (in2avg.mtx) is to >> make a new matrix that just has the offsets and concatenate >> the two matrices using convert_xfm. This is slightly more complicated >> (you need to get the order right in convert_xfm) but is much >> more script-friendly. >> >> >> >> On 26 Nov 2004, at 07:22, Gaby Pell wrote: >> >>> Hi Mark, >>> >>> I seem to have a problem applying the COV shift to some registered >>> images. >>> I am registering a 250x196x250mm volume to the 182x218x182mm standard >>> brain - so I have added the calculated FOV offsets to the last >>> column's >>> x,y,z translation entries (34,-11,34mm respectively). After appplying >>> the >>> modified mat file to the original image, it is still far from being >>> centred in the image. Am I missing something? >>> >>> One clue might be that the registered image after the initial >>> registrations step does not seem to follow the rule you give of >>> (0,0,0) >>> being the origin voxel. In this image, it is only the "upper" and >>> "right"- >>> most parts of the brain that are visible and they are both lodged >>> into >>> this lower left corner. >>> >>> Thanks, >>> >>> Gaby >>> >>> On Mon, 22 Nov 2004 08:37:04 +0000, Mark Jenkinson >>> <[log in to unmask]> >>> wrote: >>> >>>> Hi Gaby, >>>> >>>> Sorry not to reply sooner. >>>> We don't have any scripts written to do this FOV correction >>>> as we've never used it ourselves. However, all you need to >>>> do is extract the FOV difference (use avwhd to get the relevant >>>> sizes) and add/subtract half of this from the last column in >>>> the registration matrix. >>>> >>>> You could also pad if you like, but the above method is >>>> probably easier. >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> >>>> On 16 Nov 2004, at 06:21, Gaby Pell wrote: >>>> >>>>> Hi Mark, >>>>> >>>>> Is there anyway to script this process for registration on multiple >>>>> volumes? >>>>> Another registration option I guess would be take the small FOV >>>>> reference >>>>> image and pad it in such a way as to keep the same voxel size but >>>>> increase >>>>> the FOV? Is this a sensible approach? >>>>> >>>>> Thanks, >>>>> >>>>> Gaby