Hi,
This is the command I use (of course, with 2 loops for going through all the subjects - 1st loop - and all the runs - 2nd loop):
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for ((i=1;i<10;i++)); do
for ((j=1; j<6; j++)); do
3dBlurToFWHM -input ${global_path}2.derivatives/sub-0${i}/func/sub-0${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz \
-prefix ${global_path}5.1st_level_analysis/sub-0${i}/func/GLM_INPUT/sub-0${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-preproc_bold_blur.nii.gz \
-mask ${global_path}2.derivatives/sub-0${i}/func/sub-0${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz \
-FWHM 6 -detrend
done
done
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And yes, as you mentioned, this command (3dBlurToFWHM) is not part of afni_proc.py; I run this command (3dBlurToFWHM) separately (with the intention to blur the preprocessing output from the fMRIPrep).
As you can see, I don't have the ACF option for this command (3dBlurToFWHM). However, as I previously mentioned, after the 3dBlurToFWHM command is completed, the 3dFWHMx command appears automatically (in order to check the quality of the 3dBlurToFWHM command), as can be seen in this output:
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+ Checking results by running command below:
+ /home/z820/abin/3dFWHMx -arith -detrend -mask /media/z820/Hard_3/SciRel/2.Analysis/2.derivatives/sub-102/func/sub-102_task-rest_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz -input /media/z820/Hard_3/SciRel/2.Analysis/5.1st_level_analysis/sub-102/func/GLM_INPUT/sub-102_task-rest_space-MNI152NLin6Asym_res-2_desc-preproc_bold_blur.nii.gz
++ 3dFWHMx: AFNI version=AFNI_23.0.07 (Mar 1 2023) [64-bit]
++ Authored by: The Bob
....
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Thank you in advance for your help!
Cheers,
r.
