Hello CAT12 experts,
I think I have an easy question but just wanted some clarification/confirmation on the CAT12 output files when running a longitudinal analysis as it’s not very clear from help section. Let’s take this scenario:
INPUT: T1.nii.gz
OUTPUT: rT1.nii.gz
OUTPUT: /mri/mrT1.nii.gz
[INTERMEDIARY: sanlmT1.nii.gz]
I’m running it in batch mode from the terminal (cat_batch_long.sh).
My question is: what processing steps have been applied to the rT1.nii.gz? As far as I can tell, it is denoised, probably bias-field corrected, and then affine coregistered (6 DOF?) to the average (intra-subject) template “avg_T1.nii.gz”. Importantly, are there any nonlinear deformation steps applied to either the rT1.nii.gz or ./mri/mrT1.nii.gz files? What are the difference between these two in terms of processing steps?
Last, a related but ancillary question; what are folks doing about applying longitudinal processing steps to cross-sectional (single scans)? Is there any way to apply an identical preprocessing to these scan? For example, Freesurfer recommends using their longitudinal processing pipeline even on single timepoint subjects so as not to bias the analysis.
Many thanks!
Chris