I am trying to restrict
fixelcfestatsto run in an roi-based manner, using a seed-to-target region that I generated fromtckgen(using the population template).
Excuse me while I mould your question a little…
Within this experiment, once you have performed a segmentation of sorts of the pathway of interest, is it still necessary to provide fixel sensitivity and specificity during the statistical analysis? I.e. Would it still be of interest if the observed statistical effect only consitituted a fraction of the bundle cross-section, or a fraction of its length?
Or would it instead be adequate to “collapse” your quantitative measure of interest (e.g. FD, FC, FDC) into a single scalar measure per subject (e.g. the mean value within the fixels corresponding to the pathway of interest), and then perform your statistical inference on those values directly rather than doing a full-blown CFE?
Reason I ask is that it wouldn’t be a whole lot of effort to implement a -mask option for fixelcfestats (which would avoid the need for the fixelcrop step), but as I thought about it I couldn’t fully rationalise it.