Profiles

To select one or multiple profiles, please use the -profile option. For example:

$> nextflow run tractoflow -r 2.4.3 --input input_folder -profile macos,fully_reproducible -with-singularity singularity_name.sif -resume

Profiles available

macos

When this profile is used, TractoFlow will modify a parameter (scratch) for MacOS users.

use_gpu

When this profile is used, TractoFlow will use eddy_cuda for Eddy process. If local tracking is also enabled, Tractoflow will use the gpu implementation of scil_compute_local_tracking.py. This feature is available with NVidia GPUs only. Without this profile, TractoFlow will run eddy_openmp.

fully_reproducible

When this profile is used, all the parameters will be set to have 100% reproducible results. This profile consist to set multi-thread parameters to be fully reproducible [Theaud20].

cbrain

When this profile is used, Nextflow will copy all the output files in publishDir and not use symlinks.

ABS

When this profile is used, TractoFlow-ABS (Atlas Based Segmentation) is used. This profile must be used for pathological data. The aparc+aseg.nii.gz and wmparc.nii.gz must be in the same space than t1.nii.gz

bundling

When this profile is used, it will activate custom tracking parameters to improve recobundle results.

connectomics

When this profile is used, it will activate custom tracking parameters to improve connectomics analysis.