warping and alignment optimization

Gentlepeople-

We’re in a spring-cleaning / optimization mood over here, particularly with respect to warping and functional-to-anatomical alignment. For each, we’d like to select an option currently in play and compare it to something that might do better. Currently, with respect to warping, we use -tlrc_NL_warp and -tlrc_base MNI152_2009_template.nii.gz, otherwise, vanilla. Is there some default you’d most suggest playing with? (e.g., -anat_uniform_method from default to unifize?) Or maybe something you have in development that you’d like us to test drive? Same question for alignment. We currently use -align_opts_aea -cost lpc+ZZ. Tweaks suggested? Feel free to suggest more than one alternative per process and we’ll permute the warping and alignment processes, do some QA, and report back!

All best,

Paul

Hi, Paul-

For aligning to a template space, as well as for skullstripping an anatomical, we have started to recommend using @SSwarper before running afni_proc.py. There is an example of using that warpage information in your subsequence afni_proc.py command in the @SSwarper help file.

For aligning EPI and anatomical, we still recommend using the lpc+ZZ cost function (I’m not sure if it is the default yet, so you can still set it explicitly). Sometimes the “giant_move” is useful, or at least the “big move”, to do center of mass alignment at the start, in case the centers of mass are far apart initially:
-align_opts_aea -cost lpc+ZZ -giant_move
(The big move is less drastic, opening up the fit parameters less; there is more risk of getting stuck in a local min with giant_move, but hopefully the “+ZZ” aspect on the cost function would help outweigh that.)

You might also want to add in the automatic checking for LR flipping between the EPI and anat:
-align_opts_aea -check_flip
Free information to check about a possible header problem in the data.

–pt

Thanks, Paul! Some juicy bits in there. We’ll take @SSwarper for a spin and report back!