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

History of AFNI updates  

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October 20, 2020 05:22PM
Hello AFNI experts!

I have two basic and quick questions,
I am not used to working with human datasets and I am surprised with the processing time with afni_proc.py
I have human BOLD images at a resolution of 2.8 and afni_proc.py takes more than 5h per subject and my computer has good characteristics.
Is that normal?

afni_proc.py -subj_id imapt1s080 -script Imapt1s080/proc.imapt1s080 -scr_overwrite -out_dir imapt1s080.results -blocks despike tshift align tlrc volreg blur mask regress -dsets Rest_BOLD.nii.gz -copy_anat anatSS.imapt1s080.nii -anat_has_skull no -tcat_remove_first_trs 5 -regress_RSFC -volreg_align_to first -volreg_align_e2a -volreg_tlrc_warp -align_opts_aea -epi_strip 3dAutomask -cost lpc+zz -giant_move -check_flip -tlrc_base MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets anatQQ.imapt1s080.nii anatQQ.imapt1s080.aff12.1D anatQQ.imapt1s080_WARP.nii -regress_motion_per_run -regress_bandpass 0.01 0.1 -blur_size 4 -regress_est_blur_detrend yes -regress_run_clustsim no -execute

Should I decrease the resolution of the BOLD prior to afni_proc to speed up the process? Losing spatial resolution is not a big deal in my study.

Also, to calculate mALFF, the result is strongly dependent on the mask used. Is there a way with afni_proc to add this mask in -regress_RSFC?
Thank you!
Clément
Subject Author Posted

BOLD resolution for afni_proc.py

Doughboys October 20, 2020 05:22PM

Re: BOLD resolution for afni_proc.py

Doughboys October 22, 2020 11:14AM

Re: BOLD resolution for afni_proc.py

ptaylor October 22, 2020 11:36AM

Re: BOLD resolution for afni_proc.py

ptaylor October 22, 2020 11:35AM

Re: BOLD resolution for afni_proc.py

Doughboys October 22, 2020 02:04PM

Re: BOLD resolution for afni_proc.py

ptaylor October 22, 2020 04:14PM

Re: BOLD resolution for afni_proc.py

Doughboys October 22, 2020 04:53PM

Re: BOLD resolution for afni_proc.py

ptaylor October 22, 2020 06:00PM

Re: BOLD resolution for afni_proc.py

Doughboys October 28, 2020 02:44PM

Re: BOLD resolution for afni_proc.py

ptaylor October 28, 2020 04:04PM

Re: BOLD resolution for afni_proc.py

Doughboys October 29, 2020 09:02PM