Hello,
I created my afni.proc script based on examples I saw on the afni website. I have ran this script on my participant's and it runs successfully. I have checked the QC html and the outputs seem good. I have two questions based on my script and QC I am planning on doing:
(1) I was wondering whether my script looks okay and whether there is anything integral missing or anything else I should add? My script is below.
(2) In terms of QC, I am going through the ss_review_driver and QC_xxx/index.html -is there anything else you recommend that I should evaluate to complete the QC?
(3) Within the ss_review_basic, I have been reviewing my participant's avg censored motion, max censored displacement and censor fraction, for high numbers. I was wondering whether there are any threshold levels I should use to potentially remove participants?
Thank you very much,
Tamara
afni_proc.py -subj_id 1422 -script proc.June2_2021 -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale regress -copy_anat \
/imaging/1422/1422.anat+orig -dsets \
/imaging/1422/1422.1+orig.HEAD \
/imaging/1422/1422.2+orig.HEAD \
/imaging/1422/1422.3+orig.HEAD \
/imaging/1422/1422.4+orig.HEAD \
/imaging/1422/1422.5+orig.HEAD \
/imaging/1422/1422.6+orig.HEAD \
-tcat_remove_first_trs 0 -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size \
6.0 -regress_stim_times \
/imaging/1422/Dfeel_Bad_NoResp.txt \
/imaging/1422/Dfeel_Bad_Resp.txt \
/imaging/Dfeel_Happy_NoResp.txt \
/imaging/Dfeel_Happy_Resp.txt \
/imaging/Feel_Bad_NoResp.txt \
/imaging/Feel_Bad_Resp.txt \
/imaging/Feel_Happy_NoResp.txt \
/imaging/Feel_Happ_Resp.txt \
/imaging/Nat_neg_NoResp.txt \
/imaging/Nat_neg_Resp.txt \
/imaging/Nat_post_NoResp.txt \
/imaging/1422/Nat_post_Resp.txt \
/imaging/1422/Rating.txt \
/imaging/1422/new.Instruct.txt \
-regress_stim_labels Dfeel_Bad_NoResp Dfeel_Bad_Resp Dfeel_Happy_NoResp \
Dfeel_Happy_Resp Feel_Bad_NoResp Feel_Bad_Resp Feel_Happy_NoResp \
Feel_Happy_Resp Nat_neg_NoResp Nat_neg_Resp Nat_post_NoResp \
Nat_post_Resp Rating Instruct \
-regress_basis dmBLOCK -regress_stim_types AM1 -regress_censor_motion \
1.0 -regress_censor_outliers 0.1 -regress_apply_mot_types demean deriv \
-regress_motion_per_run -regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no \
-regress_opts_3dD -GOFORIT 15 \
-execute
