ptsii

Thanks! I'll look at the isa stuff too. Some basic questions about splitChannels: - I see I can do something like: ``` affine_plus_warp_xvec

I see that you wrote the composed warp file to /tmp, then read it back in with antsImageRead. Does this mean that I shouldn't properly access the composed warp file...

I believe (but could be wrong) that the calculation is not right... the numbers look very odd: ``` > mytx aa=antsApplyTransforms(ri(1), ri(2),mytx$fwdtransforms,compose="/tmp/temp.nii.gz" ) > warp=splitChannels(antsImageRead(aa)) > mag=sqrt( warp[[1]]^2 + warp[[2]]^2...

Here is what the 2 images look like, plus the mag results:  I have a hard time believing the mean displacement is over 11 mm...

OK, so doing a rigid registration first, and using that as the starting point for the deformation registration, resulted in values that make sense. Thanks for all your input on...

In case it might be useful to someone in the future (its a pretty obscure question): I think I have figured out a way to address my second question, which...

After downloading as above, I did: `plot(mymni[[1]], mymni[[2]], alpha=.8)` I also note that if I threshold the MNI at values 1 and higher (which surely includes some CSF), and plot...

OK. Any thoughts about why the AAL doesn't match the MNI particularly closely (the areas were drawn on a version of the MNI, so it seems odd to me they...

That makes sense. Is there a published reference by any chance that makes this clear, that I can include in my manuscript? -Tom

On my machine it takes 20 seconds or so to render, for some reason (something about R's pdf creation engine?). Anyway, here are png versions (I'll also update the original...