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
-copy_anat $top_dir/anat.nii
-anat_has_skull no
-tcat_remove_first_trs 0
-dsets $top_dir/epi.nii
-align_opts_aea -giant_move
-tlrc_base wax_rat_T2_ns.nii.gz
-volreg_align_to first
-volreg_align_e2a
-volreg_tlrc_warp
-blur_size 4.0
-regress_censor_motion 0.3
-regress_opts_3dD
-jobs 2
-regress_est_blur_epits
-regress_est_blur_errts
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?
Thanks,
Liang
