 |
 |
Hello, Option -stages refers to the process of finding the parameters of the transformation (translations, rotations). When calculating the dissimilarity between the reference image (IREF) and the image we want to register to the reference image (IM), interpolation needs to be applied to IM. The interpolation choices in MCFLIRT are: trilinear, sinc and nearest neighbour. Different choices of the interpolation function are used for different stages of the algorithm, and sinc is used for the 4th stage (which is optional). Once the minimisation process is finished and all of the transformation parameters are estimated, a transformation is applied to the image IM. This transformation can be applied using either trilinear or sinc or the nearest neighbour interpolation method (the default in MCFLIRT is trilinear interpolation). If you specify sinc_final it will be sinc. SO in short: sinc in stages helps to find the right transformation, sinc_final applies sinc interpolation to the image when applying this transformation. Hope this helps, Ivana On 22 Dec 2010, at 19:01, Michael Waskom wrote: > Hi Mark (or whoever else might know), > > Could you help me understand the various options pertaining to sinc > interpolation in MCFLIRT? Looking at the usage in version 4.1.6, it > seems that there are two different options, "-sinc_final" and setting > the "-stages" argument to 4. Running MCFLIRT with a permutation of > these flags (in other words, calling it three times with the same > input and reference volume but using both, or either one in isolation) > seems to produce three different images (according to a diff between > them). But, what is actually going on differently in the algorithm? > Unfortunately, the online MCFLIRT user guide seems not to have any > information on the -sinc_final option. Thanks! > > Cheers, > Michael >