SET with CIVET¶

Download SET package : http://scil.dinf.usherbrooke.ca/en/containers_list/

Run civet¶

Run civet-nf¶

mkdir ~/nf/civet_test
cd ~/nf/civet_test

# Use the online CBRAIN tools and Guide
nextflow-20.04.1-all ~/nf/set_1v0/set-nf/civet-nf/main.nf \
    --civet civet_output/ \
    -with-singularity ~/nf/set_1v0/set_1v0.img \
    -resume

cd ~/nf/
sh ~/nf/set_1v0/civet-nf/tree_for_tractoflow.sh -f input_data/ -c ~/nf/civet_test -o tractoflow_pve/

Run Tractoflow (-profile civet_pve)¶

mkdir ~/nf/tf_test
cd ~/nf/tf_test

nextflow-20.04.1-all run ~/nf/set_1v0/tractoflow_stonge/main.nf \
    --root tractoflow_pve/ \
    -dti_shells "0 1000" --fodf_shells "0 1000" \
    -profile civet_pve \
    -with-singularity ~/nf/tractoflow_2.0.0_8b39aee_2019-04-26.img \
    -resume

Run SET Nextflow (set-nf)¶

nextflow-20.04.1-all run ~/nf/set_1v0/set-nf/main.nf \
    --tractoflow tractoflow_output/ \
    --surfaces freesurfer_output/ \
    -profile freesurfer_basic \
    -with-singularity ~/nf/set_1v0/set_1v0.img \
    -resume