Usage for HCP

Setup data

Run Tractoflow Nextflow (tractoflow_stonge)

mkdir /scratch/user/nf/hcp_tf_test
cd /scratch/user/nf/hcp_tf_test

nextflow -c /scratch/user/nf/singularity.conf run /scratch/user/nf/set_1v0/tractoflow_stonge/main.nf \
    --root /scratch/user/data/hcp_data/ \
    -profile brain_mask_only \
    --dti_shells "0 1000" --fodf_shells "0 1000 2000 3000" \
    --run_topup false --run_eddy false \
    --run_resample_dwi false --sh_order 8 \
    --set_frf true --manual_frf "15,4,4" \
    --run_ants_warp_t1 false run_resample_t1 false \
    --run_denoise_t1 true --run_n4_t1 false \
    --run_dwi_denoising true --processes_denoise_dwi 8 \
    -with-report report.html \
    -with-singularity /scratch/user/nf/tractoflow_2.0.0_8b39aee_2019-04-26.img \
    -resume

Run SET Nextflow (set-nf)

mkdir /scratch/user/nf/hcp_set_test
cd /scratch/user/nf/hcp_set_test

nextflow-20.04.1-all -c /scratch/user/nf/singularity.conf run /scratch/user/nf/set_1v0/set-nf/main.nf \
    --tractoflow /scratch/user/nf/hcp_tf_test/results/ \
    --surfaces /scratch/user/data/hcp_freesurfer/ \
    --nowarp true \
    -profile civet2_dkt \
    -with-report report.html \
    -with-singularity /scratch/user/nf/set_1v0/set_1v0.img \
    -resume