fmri preprocessing on phantom

MayaSa · May 9, 2023, 9:13am

Hi,
I am trying to conduct some analyses on phantom data (SE acquisition on 7T), but having trouble with applying minimal preprocessing stages. The main things I need to perform are detrending and scaling.
Do you have any ideas on how to make this work on phantom data?

Thank you in advance,
Maya

rickr · May 9, 2023, 1:45pm

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