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fMRI_Analysis_AFNI_Unix_Matlab

AFNI pre-processing, 1st level statistics and ROI analysis:

fMRI_Preprocessing_Statistics_Recon.txt

  • Creates afni_proc.py for every subject specified including pre-processing steps (re-alignment, outlier analysis, spatial smoothing, mean scaling, 1st level statistical regression model)
  • Does SUMA surface reconstruction
  • Runs individual models with additional first level models
  • Creates anatomical ROIs by selecting certain regions from an atlas
  • Creates functional ROIs by selecting active Voxels for certain conditions
  • Creates anatomical/functional ROIs by merging functional and antomical ROIs
  • Calculates and extracts percent signal values from statistical maps from individual ROIs

Automated SUMA controller:

Create_Contrast_ROI_images.txt

  • Creates selected fMRI contrasts per subject calls SUMA displays contrast on individual reconstructed brain surface and saves a jpg of left and right hemisphere as lateral and medial view in designated location
  • Loads individual ROIs (anatomical and/or functional) per subject calls SUMA displays ROI on individual reconstructed brain surface and saves a jpg of left and right hemisphere as lateral and medial view in designated location

General regressor files for AFNI

Noisy_Audiovisual_Regressors.m

  • Creates regressor files for specified conditions and onsets for two experiments

Individual regressor files for AFNI

Noisy_Audiovisual_Regressors_Individual_Response.m

  • Creates regressor files for specified conditions and onsets for two experiments
  • Takes individual behavior into account and creates regressors for individual subjects

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