Hi, Sam-

Great, glad the IT was accommodating so quickly.

Thanks for sending those images---that helps show that the initial overlap is quite good, both initially and after the center-of-mass shift (perhaps some center-of-mass alignment had already even been done, esp. judging by the input filename? Fine.). Actually, that was the main thing that I thought might be going awry here. The tissue contrast+resolution of the input dataset also seems fine, so that shouldn't be creating a problem for alignment.

It also appears that your anatomical was skullstripped already. That isn't a problem, just something to note (@animal_warper itself would accomplish that, too).

I was going to ask to also see the init_qc_02*jpg that should be created---that shows the result of affine alignment. However, I can in the text about the image generation that underlay range is set to [0, 0], which means the dataset isn't even in the FOV... which means that something bad happened in the affine alignment step.

And, interestingly, the date of your binary set's compilation is Sept 27, 2021. That is somewhat old, but more importantly we introduced a (re)stabilizing change to a couple affine alignment cost functions in 3dAllineate on Sept 29, 2021, and I think that this is the kind of situation those changes would prevent.

So, the TL;DR now after you've read this far: I suspect if you update your AFNI binaries, you won't have this trouble with the alignment. (A side benefit: I also made a change just recently so that @animal_warper should exit on the first failure it gets, rather than continuing on, to make debugging simpler.) On a standard system, you could just run:

@update.afni.binaries -d

... to accomplish this.

On your administered system, actually it would be good if the admins could more regularly update AFNI (say, once a quarter or twice a year, at a minimum?). But even if you are on an administered system, you can still install the binaries on to your local directory and put that location at the start of your path, and then you will be using that local version of the binaries---and you can update that whenever you want, because admin rights are needed for it. How does that sound? If that is appealing but you have questions about the mechanics of doing so, we can help with that, too.

--pt



Edited 1 time(s). Last edit at 03/03/2023 12:20PM by ptaylor.