Dear AFNI experts,
I have one T2 weighted anatomical data of rat brain and one resting-state fMRI data.
How can I perform the resting state fMRI preprocess pipeline on the rat’s data?
The 3dSkullStrip failed with the default parameters, I tried to add -rat in the 3dSkullStrip.
3dSkullStrip -input anat.nii -prefix anat_striped_s.nii -rat
But some parts of the rat brain were missed(the picture is attached).
other parameters -ld 30 and -ld 50, -shrink_fac 0.3 did not make the result better.
The processing script is generated by afni_proc.py with the following parameters.
afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite
-blocks tshift align tlrc volreg blur mask scale regress
If this script were suitable for the rat brain?
How can I perform the registration method in this paper (Registering and analyzing rat fMRI data in the stereotaxic framework by exploiting intrinsic anatomical features - ScienceDirect, Registering and analyzing rat fMRI data in the stereotaxic framework by exploiting intrinsic anatomical features) which claimed available in AFNI?