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FINTA Flow is a nextflow pipeline using the FINTA approach for white matter bundles recognition in tractography.
To use this pipeline you must have access to 6 documents - namely:
- best_model_ae.pt
- finta_multibundles.sif
- mni_masked.nii.gz
- rbx_atlas (folder containing WM atlas bundles, AC.trk, AF_L.tr, ...)
- rbx.json
- thresholds_ae.json
If you use this pipeline, please cite:
Legarreta, J. H. et al. Filtering in tractography using autoencoders (FINTA). Medical Image Analysis 72, 102126 (2021)
- Nextflow
To launch the pipeline you can run:
nextflow run main.nf --input inputs/ --model /path/to/best_model_ae.pt --atlas_config /path/to/rbx.json --atlas_anat /path/to/mni_masked.nii.gz --atlas_directory /path/to/rbx_atlas/ --atlas_thresholds /path/to/thresholds_ae.json -with-singularity /path/to/finta_multibundles.sif -resume
See USAGE or run nextflow run main.nf --help