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Great, thank you Mark. Martin On Oct 22, 2011 2:23 AM, "Mark Jenkinson" <[log in to unmask]> wrote: > Dear Martin, > > The refvol is used to determine the ROI used for calculating the > rms difference over. Essentially it specifies the centre for a > sphere of radius 80mm. It normally doesn't make a huge > difference to the results what is chosen, unless there are big > rotations and translations. I often use the input image here, > especially if there is a huge difference in FOV, but as I said > it doesn't matter much. > > If you want to measure the "amount" of transformation going > on then comparing with the identity matrix is very sensible. > > All the best, > Mark > > > > > > On 22 Oct 2011, at 04:25, Martin M Monti wrote: > > > Dear FSLers, > > > > I have two quick questions on the use of rmsdiff: I am trying to get a > single measure of "how much" sheering/translating/etc there was across a set > of (linear) registrations. > > 1. I am a little confused by what would be 'refvol' in the command's > syntax. In other commands refvol is the "to" image(i.e., in > example_func2highres it would be the "highres"), but on the manual online > it's referred to as an "input image" which would make me think of > "example_func". So is it the "from" or "to" image I need there? > > 2. I am not comparing different registrations for the same image, rather > I would just like to get a number as to, for each of my subjects, how much > moving around there was. Would it be fair game to use an identity matrix > (for all my subjects) as the second input matrix? Naively, I'd think this > would give me a common "no registration" benchmark for all the subjects. > > > > thank you > > > > Martin > > > > > > -- > > Martin M Monti, PhD > > Assistant Professor > > 7461E Franz Hall > > UCLA Department of Psychology > > BOX 951563, > > Los Angeles, CA 90095-1563 > > 310-825-8546 > > http://montilab.psych.ucla.edu > > http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3 < > http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3%20> > > > > “Well! I’ve often seen a cat without a grin,” thought Alice, > > “but a grin without a cat! It’s the most curious thing I ever > > saw in my life!” [Lewis Carroll, Alice in Wonderland] > > >