AlzheimersOnGNN

Note: All scripts run from the repo root directory

Init environment

conda create -n alz python=3.9
pip install -r requirements.txt

Install Clinica Dependencies

Download dcm2niix

conda install -c conda-forge dcm2niix

Download SPM12:

mkdir thirdparty && cd thirdparty
wget --no-check-certificate https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip
wget --no-check-certificate https://www.fil.ion.ucl.ac.uk/spm/download/spm12_updates/spm12_updates_r7771.zip
unzip spm12.zip
unzip -o spm12_updates_r7771.zip -d spm12

Download Matlab, and don't forget to call inside Matlab once (modify PREFIX_PATH):

addpath('PREFIX_PATH/thirdparty/spm12')
spm

Download Necessary Data

1. Download ADNI MRI Data: (unzipped directory named currently as ADNI_MRI_Source_rs-fMRI_BIDS including folders of subjects)
2. Download ADNI Clinical Data (unzipped directory named currently as clinical_data_merged including number of CSV files)
3. Ensure
4. Modify paths if different in convert_adni_to_bids_clinica.sh and `preprocess_t1volume_adni_clinica.sh

Credits and Acknowledgements:

• https://github.com/jamiesonor/imagin
• https://github.com/egyptdj/stagin
• https://github.com/NYUMedML/CNN_design_for_AD
• https://aramislab.paris.inria.fr/clinica/docs/public/latest/Third-party/