├── README.md
├── LICENSE.txt
├── data
|   ├── fid_standards
|   ├── input_fid_MNI_linear_combined
|   ├── input_fid_native
|   ├── OASIS-1
|   └── demographics.tsv
├── manuscript
|   ├── afids_glass_brain.html                      # Interactive glass brain plot of all AFIDs
|   └── final_figures                               # Final manuscript figures
├── results
|   ├── avg_fcsv
|   └── plots
└── src
    ├── matlab
    |    ├── Fids_analysis.m                        # AFIDs analysis in patient space 
    |    ├── Fids_analysis_fmriprep.m               # AFIDs analysis using fmriprep results
    |    ├── Fids_analysis_mni.m                    # AFIDs analysis in MNI space 
    |    └── Fids_distance.m                        
    └── python
        ├── antsApplyH5TransformsToSlicerFCSV.py    # applies full ANTS transform to fcsv file of markups points using the **antsApplyTransformsToPoints** ANTS command 
        ├── antsApplyLinearTransformToSlicerFCSV.py # applies linear component of ANTS transform to fcsv file of markups points using the **antsApplyTransformsToPoints** ANTS command 
        ├── apply_transform.py                      # to be run within 3D Slicer Python interactor - applies transform to all input fcsv files
        ├── Fids_analysis.py                        # manuscript analysis and figures
        ├── registration_decoupling.py              # code used to decouple the linear and non-linear components of the ANTS transform using the **CompositeTransformUtil** ANTS command
        └── requirements.txt