Hi Rick,

Ok, thank you this is helpful. Below you will find my proc.py command. I modified example 11 to include bandpass filtering (0.01-0.1 Hz) in addition to motion and outlier censoring. Is it correct that while running the proc.py script the TR will be read from the EPI input (NIFTI) header? By including bandpassing in the pipeline with the wrong TR, I am affecting the DOF that are retained, correct?

afni_proc.py                                                                                                            \
                 -subj_id ${sid} -script proc.${sid} -scr_overwrite -out_dir ${sid}.results                      \
                 -blocks despike tshift align tlrc volreg blur mask scale                                               \
                     regress                                                                                                                   \
                 -radial_correlate_blocks tcat volreg                                                                           \
                 -copy_anat ${ss_dir}/anatSS.${sid}.nii                                                                       \
                 -anat_has_skull no                                                                                                     \
                 -anat_follower anat_w_skull anat  ${ss_dir}/anatU.${sid}.nii                                      \
                 -anat_follower_ROI aaseg anat ${fs_dir}/aparc.a2009s+aseg.nii.gz                         \
                 -anat_follower_ROI aeseg epi ${fs_dir}/aparc.a2009s+aseg.nii.gz                            \
                 -anat_follower_ROI FSvent epi ${fs_dir}/fs_ap_latvent.nii.gz                                     \
                 -anat_follower_ROI FSWe epi ${fs_dir}/fs_ap_wm.nii.gz                                           \
                 -anat_follower_erode FSvent FSWe                                                                           \
                 -dsets ${raw_epi}                                                                                                        \
                 -tcat_remove_first_trs 4                                                                                             \
                 -tshift_opts_ts -tpattern altplus						                                   \
                 -align_opts_aea -cost lpc+ZZ -giant_move -check_flip                                            \
                 -tlrc_base MNI152_2009_template_SSW.nii.gz                                                       \
                 -tlrc_NL_warp                                                                                                           \
                 -tlrc_NL_warped_dsets ${ss_dir}/anatQQ.${sid}.nii ${ss_dir}/anatQQ.${sid}.aff12.1D                     \
                     ${ss_dir}/anatQQ.${sid}_WARP.nii                                                                      \
                 -volreg_align_to MIN_OUTLIER                                                                              \
                 -volreg_align_e2a                                                                                                    \
                 -volreg_tlrc_warp                                                                                                     \
                 -blur_size 4                                                                                                              \
                 -mask_epi_anat yes                                                                                                \
                 -regress_motion_per_run                                                                                        \
                 -regress_ROI_PC FSvent 3                                                                                    \
                 -regress_ROI_PC_per_run FSvent                                                                         \
                 -regress_make_corr_vols aeseg FSvent                                                                 \
                 -regress_anaticor_fast                                                                                            \
                 -regress_anaticor_label FSWe                                                                               \
                 -regress_censor_motion 0.3										        \
 	      	 -regress_censor_outliers 0.1										        \
		 -regress_bandpass 0.01 0.1                                                                                  \
                 -regress_apply_mot_types demean deriv                                                              \
                 -regress_est_blur_epits                                                                                          \
                 -regress_est_blur_errts                                                                                          \
                 -html_review_style pythonic

I am using data from the ADNI database. In their help forum, they stated that values in the DICOM headers are checked for protocol compliance. In some instances, after converting to NIFTI, participants' NIFTI/JSON files state that the TR is equal to 6s when the DICOM header states that the TR is equal to 3 seconds. Three seconds is more aligned with the protocol documents provided by ADNI. Should I update the TR information in the NIFTI header for these participants?

Thanks,
Jenna