├── .actrc ├── .devcontainer ├── devops │ ├── Dockerfile │ ├── devcontainer.json │ ├── onCreateCommand.sh │ └── updateContentCommand.sh └── prototyping │ ├── Dockerfile │ ├── devcontainer.json │ ├── initializeCommand.sh │ ├── onCreateCommand.sh │ └── updateContentCommand.sh ├── .ecrc ├── .editorconfig ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── usage_issue.md ├── PULL_REQUEST_TEMPLATE │ ├── bugfix.md │ ├── improvement.md │ ├── new_module.md │ └── new_subworkflow.md ├── actions │ └── merge-queue-status │ │ ├── README.md │ │ └── action.yml ├── events │ └── merge_group.json ├── pull_request_template.md ├── reviewers.yml └── workflows │ ├── assign_reviewers.yml │ ├── lint_component.yml │ ├── manual_checks.yml │ ├── merge_queue.yml │ ├── publish_extension.yml │ ├── run_checks_suite.yml │ ├── test_component.yml │ ├── update_main.yml │ └── update_pr.yml ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode ├── extension-package │ ├── .vscodeignore │ ├── CHANGELOG.md │ ├── LICENSE │ ├── README.md │ ├── icon.avif │ ├── package-lock.json │ ├── package.json │ └── vsc-extension-quickstart.md └── settings.json ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── assets └── multiqc_config.yml ├── config └── resources.config ├── cspell.json ├── docs ├── astro │ ├── convert_module.py │ ├── convert_subworkflow.py │ └── templates │ │ ├── module.md.jinja2 │ │ └── subworkflow.md.jinja2 ├── cspell │ └── neuroscience.txt └── images │ ├── nf-neuro_logo_dark.png │ ├── nf-neuro_logo_dark.svg │ ├── nf-neuro_logo_light.png │ └── nf-neuro_logo_light.svg ├── modules ├── environment-schema.json ├── meta-schema.json ├── nf-neuro │ ├── betcrop │ │ ├── antsbet │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── dwi2mask │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── nextflow.config │ │ ├── fslbetcrop │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_t1.config │ │ │ │ ├── nextflow_t1_dilate.config │ │ │ │ └── tags.yml │ │ └── synthstrip │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bundle │ │ ├── centroid │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── coloring │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── fixelafd │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── labelmap │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── recognize │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_params.config │ │ │ │ └── tags.yml │ │ ├── stats │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_covariates.config │ │ │ │ ├── nextflow_lesions.config │ │ │ │ ├── nextflow_light.config │ │ │ │ └── tags.yml │ │ └── uniformize │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_axis.config │ │ │ ├── nextflow_centroid.config │ │ │ └── tags.yml │ ├── connectivity │ │ ├── afdfixel │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── decompose │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── visualize │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── denoising │ │ ├── mppca │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── nlmeans │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── harmonization │ │ └── clinicalcombat │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_clinic.config │ │ │ └── nextflow_pairwise.config │ ├── image │ │ ├── applymask │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── burnvoxels │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── convert │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow_float32.config │ │ │ │ ├── nextflow_uint8.config │ │ │ │ └── tags.yml │ │ ├── cropvolume │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_bbox.config │ │ │ │ └── tags.yml │ │ ├── math │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── addition.config │ │ │ │ ├── lower_threshold.config │ │ │ │ ├── lower_threshold_no_value.config │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── normalize_max.config │ │ │ │ ├── subtraction.config │ │ │ │ └── tags.yml │ │ ├── powderaverage │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow_noshells.config │ │ │ │ ├── nextflow_shells.config │ │ │ │ └── tags.yml │ │ └── resample │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow_isomin.config │ │ │ ├── nextflow_nn.config │ │ │ ├── nextflow_ref.config │ │ │ ├── nextflow_volsize.config │ │ │ ├── nextflow_voxsize.config │ │ │ └── tags.yml │ ├── io │ │ ├── nii2dcm │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── readbids │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── preproc │ │ ├── eddy │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── gibbs │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── n4 │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_dwi.config │ │ │ │ └── tags.yml │ │ ├── normalize │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_with_dti_shells.config │ │ │ │ └── tags.yml │ │ └── topup │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── qc │ │ ├── gif │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_4D.config │ │ │ │ └── tags.yml │ │ ├── multiqc │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── multiqc_config.yaml │ │ │ │ └── nextflow_single-subject.config │ │ └── tractogram │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── reconst │ │ ├── diffusivitypriors │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── dtimetrics │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_light.config │ │ │ │ └── tags.yml │ │ ├── fodf │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_msmt.config │ │ │ │ ├── nextflow_no_metrics.config │ │ │ │ ├── nextflow_shells.config │ │ │ │ └── tags.yml │ │ ├── freewater │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_compute_only.config │ │ │ │ ├── nextflow_priors.config │ │ │ │ └── tags.yml │ │ ├── frf │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_msmt.config │ │ │ │ ├── nextflow_msmt_set_frf.config │ │ │ │ ├── nextflow_set_frf.config │ │ │ │ └── tags.yml │ │ ├── ihmt │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── meandiffusivitypriors │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── meanfrf │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── noddi │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow_compute_only.config │ │ │ │ ├── nextflow_extract_metrics.config │ │ │ │ ├── nextflow_extract_metrics_priors.config │ │ │ │ └── tags.yml │ │ ├── qball │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_light.config │ │ │ │ └── tags.yml │ │ ├── shmetrics │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── shsignal │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── registration │ │ ├── anattodwi │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── ants │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_no_warp.config │ │ │ │ ├── nextflow_quick.config │ │ │ │ └── tags.yml │ │ ├── antsapplytransforms │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── convert │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── easyreg │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── synthmorph │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── tractogram │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── keep_invalid.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── suffix.config │ │ │ └── tags.yml │ ├── segmentation │ │ ├── fastseg │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── fastsurfer │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── freesurferseg │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── fslobes │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── fsreconall │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_debug.config │ │ │ │ └── tags.yml │ │ └── synthseg │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow_basic.config │ │ │ ├── nextflow_options.config │ │ │ └── tags.yml │ ├── stats │ │ ├── mergejson │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── metricsinroi │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_covariates.config │ │ │ ├── nextflow_csv.config │ │ │ ├── nextflow_label.config │ │ │ └── tags.yml │ ├── tracking │ │ ├── localtracking │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow_fa.config │ │ │ │ ├── nextflow_wm.config │ │ │ │ └── tags.yml │ │ ├── pfttracking │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow_fa.config │ │ │ │ ├── nextflow_interface.config │ │ │ │ ├── nextflow_wm.config │ │ │ │ └── tags.yml │ │ └── tractoracle │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── tractogram │ │ ├── densitymap │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow_mask.config │ │ │ │ └── tags.yml │ │ ├── math │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ ├── nextflow_fail.config │ │ │ │ └── tags.yml │ │ ├── removeinvalid │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── resample │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow_centroid.config │ │ │ ├── nextflow_tractogram.config │ │ │ └── tags.yml │ └── utils │ │ ├── dwishell │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow_out_indices.config │ │ │ ├── nextflow_single_shell.config │ │ │ ├── nextflow_two_shells.config │ │ │ └── tags.yml │ │ ├── extractb0 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_all4d.config │ │ │ ├── nextflow_allseries.config │ │ │ ├── nextflow_clusterfirst.config │ │ │ ├── nextflow_clustermean.config │ │ │ ├── nextflow_mean.config │ │ │ └── tags.yml │ │ └── templateflow │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── templateflow.py │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── no_brain_mask.config │ │ └── tags.yml └── yaml-schema.json ├── nf-test.config ├── package.json ├── poetry.lock ├── poetry.toml ├── pyproject.toml ├── subworkflows ├── nf-neuro │ ├── anatomical_segmentation │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── synthseg.config │ │ │ └── tags.yml │ ├── atlas_iit │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── nextflow.config │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── atlas_roimetrics │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── nextflow.config │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── bundle_seg │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── synthmorph.config │ │ │ └── tags.yml │ ├── io_bids │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── load_test_data │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── output_template_space │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── local.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── no_brain_mask.config │ │ │ ├── synthmorph.config │ │ │ └── tags.yml │ ├── preproc_dwi │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── preproc_t1 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_quick.config │ │ │ ├── nextflow_skip_all.config │ │ │ ├── nextflow_synthstrip.config │ │ │ └── tags.yml │ ├── reconst_fw_noddi │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── expect_error.config │ │ │ ├── fw.config │ │ │ ├── fw_custom_priors.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── noddi.config │ │ │ ├── noddi_custom_priors.config │ │ │ ├── noddi_fw.config │ │ │ ├── noddi_fw_avg_priors.config │ │ │ └── noddi_fw_custom_priors.config │ ├── registration │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── ants.config │ │ │ ├── easyreg.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── synthmorph.config │ │ │ └── tags.yml │ ├── topup_eddy │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── tractoflow │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── modules.config │ │ ├── nextflow.config │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── tractometry │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── nextflow_lesion.config │ │ └── 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