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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September 14, 2020 11:34AM
Hi all!

I have a decision-making experiment where I present a stimulus (for 500 ms) and then subjects make a binary decision by pressing a button (1 or 2) within 2 s. Afterwards there are other irrelevant (for my analysis) stimuli, accounting for ~13 s, and then the next trial starts. I acquire data all over the experiment (TR = 2.2s).

I am trying to analyze the fMRI data associated to two different conditions: whether the decision is correct or whether it is wrong. My design should be model-based, as the order of trials (correct vs. incorrect) depends on the subjects' responses. However, I couldn't find tutorials on how to perform this analysis in AFNI. The afni_proc.py script I put together (below) gives very random results (significant areas mostly outside the brain). Stim files are text files with one rows per TR, and 1 if it is the TR with onset at the stimulus that leads to correct/incorrect decision, or 0 otherwise.

Do you have any suggestions on how to model this analysis in AFNI? I have been bouncing my head on this problem for months!

Thanks!
Davide

afni_proc.py -subj_id $SUBJ                                                  \
        -script proc.$SUBJ -scr_overwrite                                    \
        -blocks despike tshift align tlrc volreg blur mask scale regress     \
        -copy_anat $top_dir/$SUBJ/T1w_deobliqued.nii                         \
        -tcat_remove_first_trs 2                                             \
        -dsets $top_dir/$SUBJ/ep_*_deobliqued.nii.gz                         \
        -volreg_align_to MIN_OUTLIER                                         \
        -volreg_align_e2a                                                    \
        -volreg_tlrc_warp                                                    \
        -tshift_opts_ts -tpattern alt+z                                      \
        -blur_size 4.0                                                       \
        -regress_use_stim_files                                              \
        -regress_stim_files                                                  \
            $top_dir/$SUBJ/"$SUBJ"_correct_stim_file.1D                      \
            $top_dir/$SUBJ/"$SUBJ"_incorrect_stim_file.1D                    \
        -regress_stim_types file                                             \
        -regress_stim_labels                                                 \
            correct incorrect                                 \
        -regress_basis SPMG3                                                 \
        -regress_motion_per_run                                              \
        -regress_censor_motion 1.0                                           \
        -regress_censor_outliers 0.03                                        \
        -regress_opts_3dD                                                    \
            -gltsym 'SYM: correct -incorrect' -glt_label 1 correct-incorrect \
            -jobs 8                                                          \
        -regress_make_ideal_sum sum_ideal.1D                                 \
        -regress_est_blur_epits                                              \
        -regress_est_blur_errts                                              \
        -regress_run_clustsim no                                             \
end
Subject Author Posted

Model-based fMRI for decision-making

Davide Valeriani September 14, 2020 11:34AM

Re: Model-based fMRI for decision-making

rick reynolds September 24, 2020 01:03PM

Re: Model-based fMRI for decision-making

Davide Valeriani September 24, 2020 03:32PM

Re: Model-based fMRI for decision-making

rick reynolds October 01, 2020 03:33PM

Re: Model-based fMRI for decision-making

Davide Valeriani October 05, 2020 11:41AM

Re: Model-based fMRI for decision-making

rick reynolds October 28, 2020 02:22PM

Re: Model-based fMRI for decision-making

Davide Valeriani November 09, 2020 06:43PM

Re: Model-based fMRI for decision-making

rick reynolds November 16, 2020 11:42AM

Re: Model-based fMRI for decision-making Attachments

Davide Valeriani November 17, 2020 09:39AM