AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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tamtam
July 23, 2021 09:20PM
Hello,

I would like to incorporate the -big_move function to help align my epi and anat data better, though I am not sure where I should include this option in my script. Any help is appreciated!

Thank you,
Tamara

afni_proc.py -subj_id 1423 -script proc.big_July_2021 -scr_overwrite -blocks \
tshift align tlrc volreg blur mask scale regress -copy_anat \
/imaging/Tamara/Youth/1423/1423.anat+orig -dsets \
/imaging/Tamara/Youth/1423/1423.1+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.2+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.3+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.4+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.5+orig.HEAD \
/imaging/Tamara/Youth/1423/1423.6+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/Tamara/Youth/1423/Dfeel_Bad_NoResp.txt \
/imaging/Tamara/Youth/1423/Dfeel_Bad_Resp.txt \
/imaging/Tamara/Youth/1423/Dfeel_Happy_NoResp.txt \
/imaging/Tamara/Youth/1423/Dfeel_Happy_Resp.txt \
/imaging/Tamara/Youth/1423/Feel_Bad_NoResp.txt \
/imaging/Tamara/Youth/1423/Feel_Bad_Resp.txt \
/imaging/Tamara/Youth/1423/Feel_Happy_NoResp.txt \
/imaging/Tamara/Youth/1423/Feel_Happ_Resp.txt \
/imaging/Tamara/Youth/1423/Nat_neg_NoResp.txt \
/imaging/Tamara/Youth/1423/Nat_neg_Resp.txt \
/imaging/Tamara/Youth/1423/Nat_post_NoResp.txt \
/imaging/Tamara/Youth/1423/Nat_post_Resp.txt \
/imaging/Tamara/Youth/1423/Rating.txt \
/imaging/Tamara/Youth/1423/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
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Subject Author Posted

-big_move function

tamtam July 23, 2021 09:20PM

Re: -big_move function

Peter Molfese July 26, 2021 09:18AM