- Create python environment and cloning the tigrbid-QC repo
cd /projects/ttan
module load python/3.10.7
python -m venv tigrbid_QC_env
source tigrbid_QC_env/bin/activate
pip install streamlit==1.49.1 pandas==2.3.2 pydantic==2.11.7 beautifulsoup4
git clone https://github.com/ThomasHMAC/tigrbid-QC.git- Run freesurfer QC dashboard
cd /projects/ttan/tigrbid-QC
streamlit run ./pipelines/freesurfer/fs_main.py -- --fs_metric /projects/galinejad/SCanD_CAMH_SPINS/share/freesurfer_group/euler.tsv --fmri_dir /projects/galinejad/SCanD_CAMH_SPINS/share/fmriprep/23.2.3/ --participant_labels /projects/ttan/tigrbid-QC/SPINS_participants.tsv --output_dir /projects/ttan/tigrbid-QC/outputs/SPINS_QC/- Run fmriprep QC dashboard
cd /projects/ttan/tigrbid-QC
streamlit run ./pipelines/fmriprep/fmriprep_main.py -- --fmri_dir /projects/galinejad/SCanD_CAMH_RTMSWM/share/fmriprep/23.2.3 --participant_labels /projects/ttan/RTMSWM/participants.tsv --output_dir /projects/ttan/tigrbid-QC/outputs/RTMSWM_QC/- Run Noddireg QC dashboard
cd /projects/galinejad/tigrbid-QC
streamlit run ./pipelines/noddireg/noddi_qc.py -- --noddireg_dir /projects/galinejad/SCanD_CAMH_RTMSWM/share/noddireg --participant_labels /projects/galinejad/SCanD_CAMH_RTMSWM/share/participants.tsv --output_dir /projects/galinejad/tigrbid-QC/outputs/RTMSWM_QC/- Run QSIPrep QC dashboard
cd /projects/ttan/tigrbid-QC
streamlit run ./pipelines/qsiprep/qsiprep_qc.py -- --qsiprep_dir /projects/ttan/PSIBD/data/share/qsiprep/0.22.0/ --participant_labels /projects/ttan/PSIBD/data/local/bids/participants.tsv --output_dir /projects/ttan/tigrbid-QC/outputs/PSIBD_QC_13022026- Run streamlit remotely through ssh tunnel
ssh -X -L 8501:localhost:8501 ttan@darwin.camhres.ca
cd /projects/ttan/tigrbid-QC
streamlit run ./pipelines/freesurfer/fs_main.py --server.port=8501 -- \
--fs_metric /projects/galinejad/SCanD_CAMH_SPINS/share/freesurfer_group/euler.tsv \
--fmri_dir /projects/galinejad/SCanD_CAMH_SPINS/share/fmriprep/23.2.3/ \
--participant_labels /projects/ttan/tigrbid-QC/SPINS_participants.tsv \
--output_dir /projects/ttan/tigrbid-QC/outputs/SPINS_QC/Once you run this you can open a browser on your computer and paste in the http://localhost:8501 URL