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--- biac:analysis:physiological [2022/01/20 14:46]
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+++ biac:analysis:physiological [2022/01/20 17:01]
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 RetroTS will produce "slibase" regressors to be used with retroicor during afni preprocessing, or afni retroicor regression
+=== setup afni despike, retroicor and slicetime correction ===
+<code>
+python3 /usr/local/packages/afni/21.1.04/afni_proc.py \
+ -subj_id sub-00104_run-4_ricor_phys \
+ -blocks despike ricor tshift \
+ -dsets ../../../../BIDS/sub-00104/ses-01/func/sub-00104_ses-01_task-rest_run-4_bold.nii.gz \
+ -tcat_remove_first_trs 2 \
+ -tshift_opts_ts -tpattern @/mnt/munin/BIAC/SysService.01/Analysis/UHP/BIDS/sub-00104/ses-01/physio/series004_01_slicetiming.1D \
+ -ricor_regs_nfirst 2 \
+ -ricor_regs /mnt/munin/BIAC/SysService.01/Analysis/UHP/BIDS/sub-00104/ses-01/physio/series004_01.slibase.1D \
+ -verb 1
+</code>
+The above produce an afni script to throw out 2 timepoints, perform a despike, retroicor physio regression and slice time correction based on the RetroTS output and the physio TSV/json above.
+Convert the afni corrected output back to nii.gz to be used for other pre-processing if not using AFNI for all steps
+<code>
+bxh2analyze --niigz -s pb03.sub-00104_run-4_ricor_phys.r01.tshift+orig.HEAD sub-00104_run-4_physiocorrected
+</code>

Brain Imaging & Analysis Center