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"
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" \n",
" !\n",
" Note:\n",
"
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"
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" You may see a SyntaxWarning from AFNI’s internal Python scripts when running this command — this can be safely ignored and does not affect the output.\n",
"
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"
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"
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"\n",
"Below is a brief explanation of the key options added to ```afni_proc.py```:\n",
"\n",
"```-blocks ... regress```: Adds the GLM regression step to the processing pipeline, so we can estimate condition-specific brain activity.\n",
"\n",
"```-regress_stim_times```: Points to the timing .1D files (e.g., congruent.1D, incongruent.1D) we created earlier. These specify when each condition occurred during the experiment.\n",
"\n",
"```-regress_stim_labels```: Assigns labels to the timing files. These labels are used internally in AFNI (and in our symbolic GLTs) to refer to each condition.\n",
"\n",
"```-regress_basis GAM```: Applies the canonical hemodynamic response function (HRF) using a Gamma function, which models the typical shape of neural activation over time in response to a stimulus.\n",
"\n",
"```-regress_stim_types```: *times* - indicates that the stimulus timing files list event onsets in seconds.\n",
"\n",
"```-regress_opts_3dD```: Passes additional options to the 3dDeconvolve command that runs the regression. In this case:\n",
"\n",
"```-gltsym 'SYM: +incongruent -congruent'```: Defines a contrast comparing incongruent > congruent.\n",
"\n",
"```-gltsym 'SYM: +congruent -incongruent'```: Defines the reverse contrast, congruent > incongruent.\n",
"\n",
"```-glt_label```: Assigns human-readable labels to each contrast.\n",
"\n",
"```-jobs 8```: Specifies using 8 CPU threads for faster computation.\n",
"\n",
"```-GOFORIT 0```: Prevents the script from overriding collinearity warnings in the design matrix. Useful for debugging.\n",
"\n",
"```-regress_no_motion_deriv```: Omits the temporal derivatives of the motion parameters from the regression model. These derivatives can help account for rapid or complex head motion, but may be unnecessary if the data is relatively clean or if simpler motion correction is sufficient.\n",
"\n",
"```-regress_run_clustsim no```: Disables real-time cluster-level threshold simulations, since we’re not doing single-subject inference.\n",
"\n",
"```-regress_reml_exec```: Tells AFNI to run 3dREMLfit, which uses a more sophisticated model of temporal autocorrelation. This is typically more accurate than the default 3dDeconvolve and recommended for group-level analysis later.\n",
"\n",
"```-html_review_style pythonic```: Generates a user-friendly HTML summary of the analysis, styled with Python tools.\n",
"\n",
"
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