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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p_beach
May 20, 2014 01:40PM
Hopefully a quick question about afni_proc.py

I have tlrc commands in my script setup and currently the errts output only gives me a tlrc version of the "clean" EPI data. Is there a way to get the clean EPI data in both native and tlrc space?

I guess if there isn't a way to do this then I could just run two versions of the script?

Current setup:

afni_proc.py -subj_id subj \
-dsets RestState_1+orig.HEAD RestState_2+orig.HEAD \
-copy_anat T1Volume+orig \
-out_dir subj.results \
-blocks despike tshift align tlrc volreg blur mask regress \
-tlrc_base MNI_avg152T1+tlrc \
-tlrc_opts_at -dxyz 3 \
-align_opts_aea -cost nmi \
-tcat_remove_first_trs 2 \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_align_to last \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_censor_motion 0.38 \
-regress_censor_outliers 0.1 \
-regress_bandpass 0.009 0.08 \
-regress_apply_mot_types demean deriv \
-regress_compute_tsnr yes \
-regress_ROI WMe CSFe WM CSF \
-regress_run_clustsim no \
-regress_use_tproject yes \
-regress_est_blur_errts
tcsh -xef proc.subj |& tee output.proc.subj

Thanks!
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Subject Author Posted

keeping native & tlrc EPI with afni_proc.py

p_beach May 20, 2014 01:40PM

Re: keeping native & tlrc EPI with afni_proc.py

rick reynolds May 20, 2014 02:19PM

Re: keeping native & tlrc EPI with afni_proc.py

p_beach May 20, 2014 02:27PM