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Run the FreeSurfer recon-all pipeline and create the customize freesurfer, brainnetome and glasser connectivity atlas in native space.
If you use this pipeline, please cite:
Fischl, Bruce. "FreeSurfer." Neuroimage 62.2 (2012)
https://dx.doi.org/10.1016%2Fj.neuroimage.2012.01.021
Kurtzer GM, Sochat V, Bauer MW Singularity: Scientific containers for
mobility of compute. PLoS ONE 12(5): e0177459 (2017)
https://doi.org/10.1371/journal.pone.0177459
P. Di Tommaso, et al. Nextflow enables reproducible computational workflows.
Nature Biotechnology 35, 316–319 (2017) https://doi.org/10.1038/nbt.3820
If you are on Linux, we recommend using the Singularity to run tractometry_flow pipeline.
If you have Apptainer (Singularity), launch your Nextflow command with:
-with-singularity ABSOLUTE_PATH/scilus-freesurfer-2.1.0.sif
Image is available here
If you are on MacOS or Windows, we recommend using the Docker container to run tractometry_flow pipeline.
Launch your Nextflow command with:
-with-docker scilus/scilus-freesurfer:2.1.0
The official release 2.1.0 is NOT available now.
Please, either build the singularity container using this command:
singularity build scilus-freesurfer-dev.sif docker://scilus/scilus-freesurfer:dev
and then launch your Nextflow command with:
-with-singularity ABSOLUTE_PATH/scilus-freesurfer_dev.sif
Or launch your Nextflow command with docker:
-with-docker scilus/scilus-freesurfer:dev
See USAGE or run nextflow run main.nf --help