I have a large set of clinical 2D T1 images that I would like to warp to a standard space for automated segmentation. Are there any AFNI tools that I can use for this?
If you look at the 3dQwarp help, you can search for “2D” to see more information about doing this.
–pt
You don’t give enough information to provide a better answer than Paul has given. Are these a single 2D image per subject? Or a collection of 2D images per subject, with very thick slices (say 5 mm thick, with 1 mm in plane resolution)?
These are 1 mm in plane resolution clinical T1 with whole brain coverage.
The difficulty with such volumes is that the through-slice resolution is typically 5 mm, which makes the in-slice images look good (very high SNR), but makes it hard to match them to a template dataset at 1 mm resolution. It is possible to resample them to a 1 mm grid in all 3 directions (“isotropic”), and then try the standard alignment tools. However, segmentation will be inaccurate since the resolution in the z direction will still be lousy.
If I were trying this, I would assemble the slices into a 3D dataset, then try the @SSwarper command to see how well it works. Probably a fair amount of swearing at the computer will be involved along the way.
If you need some help with this, you can upload some data, and I’ll try to take a look.