Here is the new version of the script:
#!/bin/sh
# To run this script, use the following arguments in the specified order:
#
# argument 1 - subject ID
# argument 2 - resting state dataset
# argument 3 - anatomical dataset
afni_proc.py \
-subj_id $1 \
-dsets $2 \
-copy_anat $3 \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-tcat_remove_first_trs 3 \
-align_opts_aea -cost lpc+zz \
-Allineate_opts -source_automask+4 \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
-blur_size 6 \
-regress_anaticor \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.05 \
-regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts
The old version doesn't have the line starting with -align_opts_aea -cost...
Edited 2 time(s). Last edit at 10/05/2022 11:42AM by ptaylor.
