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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May 09, 2023 09:45AM
Hi Maya,

You could run afni_proc.py on the EPI datasets, just telling it to do the scale and regress blocks:

afni_proc.py -subj_id       phant.SR      \
             -dsets                 phantom*.nii  \
             -blocks                scale regress \
             -tcat_remove_first_trs 2

To get more QC out, include the volreg block, even if it should not do much.
Also, here I request running @radial_correlate on the tcat and regress data (that could be added above).

afni_proc.py -subj_id          phant.QC             \
             -dsets                    phantom*.nii         \
             -blocks                   volreg scale regress \
             -tcat_remove_first_trs    2                    \
             -volreg_compute_tsnr      yes                  \
             -radial_correlate_blocks  tcat regress

Or, just let it pretend to analyze as simple resting state. This would also include tshift and blur blocks, along with censoring. Hopefully your phantom isn't too prone to motion...

ap_run_simple_rest.tcsh -epi phantom*.nii -run_proc

Does that seem reasonable?

- rick
Subject Author Posted

fmri preprocessing on phantom

MayaSa May 09, 2023 05:13AM

Re: fmri preprocessing on phantom

rick reynolds May 09, 2023 09:45AM