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I've created a couple of examples, I guess it will aid diagnosing: -> The first schedule is here: https://gist.github.com/oesteban/8c93a6553125d17c8990 Basically, I remove the standard 8mm scale (and I think that for very small translations/rotations even the 4mm could be removed). I also increased the smoothing at each level. -> The second schedule is here: https://gist.github.com/oesteban/6e3d8777d4e1ea728f17 In this case, it is pretty much the same as before, but now I add the option 'setoption paramsubset 1 0 0 0 0 0 0 1 1 1 1 1 1' in order to only optimize scalings and skews. My problem is that this language is a bit difficult to understand. Basically I'm testing by chance. I think that, when one inserts the optimise command, the 'amount' of transformation is controlled by the last part (something of this kind: 'rel 4') but I'm not sure of the implications of this parameter. e.g. optimise 7 UA:1-4 1.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 4 I'm also unsure about the first schedule, around the end, when it tries again the identity transform. I'm not sure this is taken into account (these copy U UA commands are quite obscure to me, sorry). Thank you so much Best wishes, Oscar *______________________________________* *Oscar Esteban* PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland On 4 September 2014 18:16, Oscar Esteban <[log in to unmask]> wrote: > Sorry, I wrote schema where I should have said 'schedule' > > *______________________________________* > *Oscar Esteban* > PhD Student / Researcher > > Biomedical Image Technologies (BIT), UPM > ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid > (Spain) > +34 915 495 700 ext.4234 > > Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 > ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland > > > On 4 September 2014 16:59, Oscar Esteban <[log in to unmask]> wrote: > >> Dear all, >> >> I'd like to write a couple of schemas in order to perform registration >> with FLIRT: >> >> -> One for motion correction in dMRI datasets (6 dof, very small >> rotations/translations). I see that search angles can be limited, what >> about translations?. >> >> -> One for eddy currents correction (12 dof, nosearch, no translations): >> here, my doubt is if I can forbid translations during optimisation. >> >> My first try will be to re-use one log-file from flirt, executed as in >> the old eddy_correct script and then set there my options. I think I will >> be able to easily forbid translations and rotations, looking at the other >> files. However, I don't know how to limit the amount of translation. >> >> Best >> Oscar Esteban >> >> *______________________________________* >> *Oscar Esteban* >> PhD Student / Researcher >> >> Biomedical Image Technologies (BIT), UPM >> ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid >> (Spain) >> +34 915 495 700 ext.4234 >> >> Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 >> ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland >> > >