├── LICENSE ├── README.md ├── Vagrantfile ├── analysis ├── Bayesian │ ├── BayesianGLM.ipynb │ ├── BayesianInference.ipynb │ ├── VariationalBayes.ipynb │ └── spm_bayesian │ │ ├── Cbeta_0001.nii │ │ ├── Hp_0001.nii │ │ ├── RPV.nii │ │ ├── ResMS.nii │ │ ├── SPM.mat │ │ ├── beta_0001.nii │ │ ├── con_0001.nii │ │ ├── mask.nii │ │ └── spmP_0001.nii ├── MVPA │ ├── ClassificationAnalysis-Haxby.ipynb │ ├── ClassificationAnalysis-orientation.ipynb │ ├── CogNeuro2017 │ │ ├── ClassficationAnalysis-attention.ipynb │ │ ├── ClassficationAnalysis-attention.py │ │ └── data │ │ │ ├── design.mat │ │ │ ├── lv1_r2.mat │ │ │ ├── lv1_tseries.mat │ │ │ ├── rv1_r2.mat │ │ │ └── rv1_tseries.mat │ ├── RSA.ipynb │ ├── get_haxby_info.py │ ├── haxby_data.py │ ├── make_event_files_from_json.py │ └── orientation_data │ │ ├── All_groups.txt │ │ ├── All_instances.txt │ │ ├── V1_groups.txt │ │ ├── V1_instances.txt │ │ ├── V2_groups.txt │ │ ├── V2_instances.txt │ │ ├── V3_groups.txt │ │ └── V3_instances.txt ├── RTmodeling │ └── RTmodeling.ipynb ├── __init__.py ├── connectivity │ ├── BayesNet.ipynb │ ├── ConnectivitySimulations.ipynb │ ├── DCM.ipynb │ ├── DCM_Amtx.png │ ├── DCM_BCmtx.png │ ├── DCM_BMS.png │ ├── GrangerCausality.ipynb │ ├── PPI.ipynb │ ├── dcm_sim.py │ ├── dcmfiles │ │ ├── SPM.mat │ │ ├── VOI_ROI0_1.mat │ │ ├── VOI_ROI0_eigen.nii │ │ ├── VOI_ROI0_mask.nii │ │ ├── VOI_ROI1_1.mat │ │ ├── VOI_ROI1_eigen.nii │ │ ├── VOI_ROI1_mask.nii │ │ ├── VOI_ROI2_1.mat │ │ ├── VOI_ROI2_eigen.nii │ │ ├── VOI_ROI2_mask.nii │ │ ├── VOI_ROI3_1.mat │ │ ├── VOI_ROI3_eigen.nii │ │ ├── VOI_ROI3_mask.nii │ │ ├── VOI_ROI4_1.mat │ │ ├── VOI_ROI4_eigen.nii │ │ └── VOI_ROI4_mask.nii │ ├── mk_model_noppi.m │ ├── mk_model_wrongppi.m │ └── run_images.sh ├── efficiency │ ├── DesignEfficiency.ipynb │ ├── DesignOptimisation.ipynb │ └── EfficiencyCorrelation.ipynb ├── firstlevel │ ├── FirstLevelModeling.ipynb │ ├── GLM.ipynb │ ├── copy_json.sh │ ├── downsample_fmri.py │ ├── fix_json.py │ ├── make_event_files_from_json.py │ ├── orig_bookdata │ │ ├── drift_olp_01_1_25_7_16.txt │ │ ├── filt_func_block_27_8_15.txt │ │ ├── gamm_acc_DM_13_S006_4D_mcf_brain_21_50_13.txt │ │ └── hrfbasisfns.txt │ └── sub00001_ses014_task002_run001_bold.json ├── group │ └── GroupAnalysis.ipynb ├── hyperalignment │ └── get_data.sh ├── introduction │ └── Introduction to notebooks, plotting, nilearn, nibabel and nipype.ipynb ├── machinelearning │ ├── Classification.ipynb │ └── MachineLearningBasics.ipynb ├── multiplecomparisons │ └── Correlation_simulation.ipynb ├── normalization │ ├── Spatial normalization.py │ └── SpatialNormalization.ipynb ├── orthogonalization │ └── orthogonalization.ipynb ├── pRFtutorial │ ├── README.md │ ├── pRF.mat │ ├── pRFCorr.m │ └── pRFCorrInstructor.m ├── postFMRIPREPmodelling │ ├── First and Second Level Modeling (FSL).ipynb │ └── First and Second Level Modeling (SPM).ipynb ├── poweranalysis │ ├── .ipynb_checkpoints │ │ └── Neuropower_demo-checkpoint.ipynb │ ├── Mask.nii 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