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Hi you just run flirt with the -applyxfm -init options: flirt -in in.img.nii.gz -ref ref.nii.gz -out out.nii.gz -applyxfm - init halfway_forward.mat That should do the trick cheers christian On 4 Apr 2007, at 11:22, Oliver Singer wrote: > Dear Mark, > thanks for your help concerning the realignment of the FA-maps > using the half-transformation matrices. Seems the best option to me. > However, I have some "technical" questions concerning the way to do > this: > I ran FLIRT on the two FA-images. Using avscale I get the matrices > for forward and backward half transform as follows: > > Forward half transform = > 0.999691 -0.024777 -0.002129 4.972743 > 0.024866 0.997103 0.071886 0.730804 > 0.000342 -0.071916 0.997410 3.274879 > 0.000000 0.000000 0.000000 1.000000 > > Backward half transform = > 0.999691 0.024866 0.000342 -4.990497 > -0.024777 0.997103 -0.071916 -0.369960 > -0.002129 0.071885 0.997411 -3.308346 > 0.000000 0.000000 0.000000 1.000000 > > My question now is how to apply these matrices to receive the > halfway-FA-images? Is it using the convert_xfm option or the > img2imgcoord option? > Sorry for this probably basic question..... > Yours Oliver > > > > > Mark Jenkinson schrieb: >> Hi, >> >> There are other interpolation schemes such as nearest neighbour >> or sinc, but they each have some disadvantages too, and will >> make one image qualitatively different from the other. The >> smoothing is inherent in trilinear interpolation, some rather >> ugly discontinuities occur with nearest neighbour and some >> ringing and/or variable smoothing can occur with sinc. >> >> An alternative is to transform both images to a half-way >> point, this equalising the interpolation effects. This is >> what is done in SIENA, and you can do the same by extracting >> the forward and backward half-transformation matrices from >> the output of "avscale" as run on your original transformation >> matrices. >> >> That's what I would recommend. >> >> All the best, >> Mark >> >> >> >>> Hi, >>> You can change the interpolation scheme to nearest neighbour. >>> (Advanced options in the gui) >>> >>> Saad. >>> >>> >>> On 2 Apr 2007, at 14:28, Oliver Singer wrote: >>> >>> >>>> Hi, >>>> >>>> I am trying to realign FA-maps of one subject, who was scanned at >>>> two different time points. After running BET I am using FLIRT for >>>> realigning (rigid body transform, 6D OF) the B0 images (extracted >>>> from the DTI data set) of the second measurement to the B0 >>>> images of >>>> the first measurement and as secondary images to apply the >>>> transform to I take the FA maps of the second measurement. >>>> The realignment works fine, but the FA-map of the second >>>> measuresment (the realigned one) was "smoothed" during the process. >>>> Since the first FA-map was not processed, the two maps differ in >>>> terms of their "resolution / smootheness". >>>> Is there a way either to turn off the "smoothing" during the >>>> realignment or to smoothe the first FA-map (which was not >>>> transformed) in a similar way? (I do not want to realign all images >>>> to a "standard brain" due to gross pathology) >>>> Any help is appreciated, >>>> >>>> Yours , Oliver >>>> >>> -------------------------------------------------------------------- >>> ---- >>> --- >>> Saad Jbabdi, >>> Postdoctoral Research Assistant, >>> Oxford University FMRIB Centre >>> >>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>> +44 (0) 1865 222545 (fax 222717) >>> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad >>> -------------------------------------------------------------------- >>> ---- >>> ____ Christian F. Beckmann University Research Lecturer Oxford University Centre for Functional MRI of the Brain (FMRIB) John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann tel: +44 1865 222551 fax: +44 1865 222717