diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 12ab8858..d4bd520d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -11,39 +11,50 @@ jobs: if: github.event.pull_request.merged == false runs-on: ubuntu-latest steps: + - name: Clone repo + uses: actions/checkout@v4 + with: + ref: ${{ github.event.pull_request.head.sha || github.base_ref }} + - name: Setup Python environment - uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.6 + uses: prefix-dev/setup-pixi@v0.8.14 with: - python-version: '3.10' - - name: yamlfix - run: poetry run poe yamlfix-check - - name: ruff - run: poetry run poe ruff-lint-check + environments: >- + dev-only + activate-environment: dev-only + + - name: isort + run: isort scattr/* -c + + - name: Black + run: black scattr --check + - name: snakefmt - run: poetry run poe snakefmt-check - test: - runs-on: ubuntu-latest - needs: [quality] - strategy: - matrix: - python-version: ['3.8', '3.9', '3.10', '3.11'] - steps: - - name: Setup Python environments - uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.6 - with: - python-version: ${{ matrix.python-version }} - install-library: true - - name: Test minimum inputs - run: poetry run poe test_base - - name: Test freesurfer input - run: poetry run poe test_freesurfer - - name: Test responsemean input - run: poetry run poe test_responsemean - - name: Test dwi input - run: poetry run poe test_dwi - - name: Test custom labelmerge inputs - run: poetry run poe test_labelmerge - - name: Test using single atlas (skipping labelmerge) - run: poetry run poe test_skip_labelmerge - - name: Test sessions - run: poetry run poe test_sessions + run: snakefmt scattr --check + + # test: + # runs-on: ubuntu-latest + # needs: [quality] + # strategy: + # matrix: + # python-version: ['3.11', '3.12', '3.13'] + # steps: + # - name: Setup Python environments + # uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.6 + # with: + # python-version: ${{ matrix.python-version }} + # install-library: true + # - name: Test minimum inputs + # run: poetry run poe test_base + # - name: Test freesurfer input + # run: poetry run poe test_freesurfer + # - name: Test responsemean input + # run: poetry run poe test_responsemean + # - name: Test dwi input + # run: poetry run poe test_dwi + # - name: Test custom labelmerge inputs + # run: poetry run poe test_labelmerge + # - name: Test using single atlas (skipping labelmerge) + # run: poetry run poe test_skip_labelmerge + # - name: Test sessions + # run: poetry run poe test_sessions diff --git a/.gitignore b/.gitignore index 818f9280..9fa69da7 100644 --- a/.gitignore +++ b/.gitignore @@ -19,3 +19,5 @@ __pycache__/ # Ruff .ruff_cache + +.pixi diff --git a/.readthedocs.yml b/.readthedocs.yml index 8fa269db..8a4fdfe7 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -17,7 +17,7 @@ formats: [pdf] build: os: ubuntu-20.04 tools: - python: '3.10' + python: '3.11' python: install: - requirements: docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt index 2f4e50c8..1047bf48 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,7 @@ -docutils<0.18 -sphinx-argparse<0.5.0 -sphinx_rtd_theme -sphinxcontrib-asciinema -myst-parser +docutils==0.17 +sphinx-argparse==0.4.0 +sphinx_rtd_theme>=1.0.0 +snakebids>=0.4.0 +myst-parser==1.0.0 +sphinxcontrib.asciinema==0.3.7 +pulp<2.8.0 \ No newline at end of file diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..ad09313d --- /dev/null +++ b/pixi.lock @@ -0,0 +1,8560 @@ +version: 6 +environments: + default: + channels: + - 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"Jason Kai ", - "Tristan Kuehn", - "Ali R. Khan", - "Roy A.M. Haast", - "Jonathan C. Lau", -] readme = "README.md" -documentation = "https://scattr.readthedocs.io" -packages = [{ include = "scattr" }] - -[tool.poetry.dependencies] -python = ">=3.8, <3.12" -snakebids = "^0.10.2" -labelmerge = "^0.4.7" -matplotlib = "^3.7.1" -nibabel = "^3.2.2" -nilearn = "^0.10.0" -niworkflows = "^1.7.9" -numpy = "^1.22.3" -pygments = "^2.15.1" -scipy = "^1.8.0" -# Required constraint for compatability with snakebids -pulp = "<2.8.0" - -[tool.poetry.group.dev.dependencies] -pytest-console-scripts = "1.2" -pytest = "^7.0.1" -poethepoet = "^0.13.1" -pre-commit = "^2.17.0" -snakefmt = "^0.6.1" -yamlfix = "^1.1.0" -ruff = "^0.1.14" - -[tool.poetry.scripts] -scattr = 'scattr.run:main' - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" - -[tool.poe.tasks] +license = "MIT" +authors = [{name = "Jason Kai, Tristan Kuehn, Roy A.M. Haast & Jonathan C. Lau", email = "tkai@uwo.ca"}] +requires-python = ">= 3.11" +dependencies = [] +scripts = { scattr = "scattr.run:app.run" } + +[package.build.backend] +name = "pixi-build-python" +version = "==0.4.0" + +[tool.pixi.workspace] +channels = ["conda-forge", "bioconda"] +platforms = ["linux-64"] + +[tool.pixi.feature.runtime.dependencies] +snakebids = ">=0.14.0,<0.15" +appdirs = ">=1.4.4,<2.0.0" +pyvista = ">=0.44.2,<0.45.0" +conda = ">=25.5.0,<26" + +[tool.pixi.feature.dev.dependencies] +flake8 = ">=4.0.1,<5.0.0" +pytest-console-scripts = ">=1.2.1,<2.0.0" +pytest = "*" +black = ">=24.0.0,<25.0.0" +pylint = ">=2.11.1,<3.0.0" +isort = ">=5.10.1,<6.0.0" +poethepoet = ">=0.10.0,<0.11.0" +snakefmt = ">=0.10.0,<0.11.0" +pygraphviz = "*" +Jinja2 = ">=3.0.3,<4.0.0" + +[tool.pixi.environments.default] +features = ["runtime"] + +[tool.pixi.environments.dev] +features = ["runtime", "dev"] + +[tool.pixi.environments.dev-only] +features = ["dev"] + +[tool.isort] +profile = "black" +multi_line_output = 3 + +[tool.pixi.pypi-dependencies] +scattr = { path = ".", editable = true } + +[tool.pixi.tasks] setup = "pre-commit install" ruff-lint = "ruff check --fix scattr" ruff-lint-check = "ruff check scattr" ruff-format = "ruff format ." snakefmt = "snakefmt scattr" snakefmt-check = "snakefmt --check scattr" -quality = ["yamlfix", "ruff-lint", "ruff-format", "snakefmt"] -quality-check = ["yamlfix-check", "ruff-lint-check", "snakefmt-check"] -test = [ - "test_base", - "test_freesurfer", - "test_responsemean", - "test_dwi", - "test_labelmerge", - "test_skip_labelmerge", - "test_sessions", -] - -[tool.poe.tasks.test_base] -shell = """ -python ./scattr/run.py ./test/data/bids ./test/data/derivatives/ participant \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_freesurfer] -shell = """ -python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \ - --freesurfer_dir ./test/data/derivatives/freesurfer \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_responsemean] -shell = """ -python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \ - --responsemean_dir ./test/data/derivatives/mrtrix/avg \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_dwi] -shell = """ -python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ \ - participant --path-dwi \ - ./test/data/derivatives/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_dwi.nii.gz \ - --path-mask \ - ./test/data/derivatives/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_mask.nii.gz \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_snakedwi] -shell = """ -python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ \ - participant --path-dwi \ - ./test/data/derivatives/snakedwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-eddy_res-orig_dwi.nii.gz \ - --path-dwi-mask \ - ./test/data/derivatives/snakedwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-eddy_res-orig_mask.nii.gz \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_labelmerge] -shell = """ -python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \ - --labelmerge_base_dir ./base_dir \ - --labelmerge_overlay_dir ./overlay_dir \ - --skip_brainstem --skip_thal_seg \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_skip_labelmerge] -shell = """ -python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \ - --skip_labelmerge --skip_brainstem --skip_thal_seg \ - --fs-license ./test/.fs_license -np --force-output -""" - -[tool.poe.tasks.test_sessions] -shell = """ -python ./scattr/run.py ./test/data/bids_sessions \ - test/data/derivatives_sessions/ participant \ - --fs-license ./test.fs_license -np --force-output -""" - -[tool.poe.tasks.yamlfix] -shell = """ -find . -type f \\( \ - -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \ - ! -iname snakebids* \ -\\) -exec yamlfix {} \\; -""" - -[tool.poe.tasks.yamlfix-check] -shell = """ -find . -type f \\( \ - -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \ - ! -iname snakebids* \ -\\) -exec yamlfix --check {} \\; -""" [tool.ruff] select = ["E", "W", "N", "RUF", "I", "UP"] diff --git a/scattr.egg-info/PKG-INFO b/scattr.egg-info/PKG-INFO new file mode 100644 index 00000000..d0bd50ba --- /dev/null +++ b/scattr.egg-info/PKG-INFO @@ -0,0 +1,71 @@ +Metadata-Version: 2.4 +Name: scattr +Version: 0.3.4rc1 +Summary: [Snakebids app] Structural connectivity between targeted regions +Author-email: "Jason Kai, Tristan Kuehn, Roy A.M. Haast & Jonathan C. Lau" +License-Expression: MIT +Requires-Python: >=3.11 +Description-Content-Type: text/markdown +License-File: LICENSE +Dynamic: license-file + +# Structural Connectivity Applied To Targeted Regions (SCATTR) +[![Documentation Status](https://readthedocs.org/projects/scattr/badge/?version=stable)](https://scattr.readthedocs.io/en/stable/?badge=stable) +![Version](https://img.shields.io/github/v/tag/khanlab/scattr?label=version) +![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10_|_3.11-blue.svg) +[![Tests](https://github.com/khanlab/scattr/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/khanlab/scattr/actions/workflows/test.yml?query=branch%3Amain) +![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/scattr) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7636506.svg)](https://doi.org/10.5281/zenodo.7636506) + +SCATTR is a BIDS App that performs a tractography processing workflow to +identify connections between targetted structures of interest (extracted from +various atlases) in the brain, using some common neuroimaging tools like +`prepdwi`, `Freesurfer`, and `Mrtrix3`. + +![Example outputs](https://raw.githubusercontent.com/khanlab/scattr/main/docs/images/ex_output.png) + +This is useful for: + +* Analyzing structural connections of known brain circuits +* Examining specific connections of interest +* Comparison across different groups (e.g. controls vs patients) + + +## Example use of workflow +This workflow was used to process and analyze the data from +[`hcp_subcortical_repo`](https://github.com/kaitj/hcp_subcortical_repro) +(see Kai et al., 2022). + +## Workflow +A brief summary of the workflow can be found below (see documentation for +a detailed summary): + +_Note: The workflow assumes Freesurfer has already been run on the dataset, as +well as diffusion preprocessing (e.g. distortion correction)._ + +![Workflow example](https://raw.githubusercontent.com/khanlab/scattr/main/docs/images/workflow.png) + +1. Merge the segmentations of structures in a standard template space from +various sources (if necessary) via +[labelmerge](https://zenodo.org/record/7636410) into a combined atlas, which is +used downstream to identify targeted connections. +1. Estimate and apply transformations from standard template space to +subject-specific space. +1. Further process the pre-processed diffusion data to enable tractography +(e.g. compute response functions, fibre orientation distribution, +normalization). +1. Perform whole-brain tractography from computed files, applying filtering +(e.g. SIFT2) to computed tractogram. Once filtered, connections between the +merged segmentations (from step 1) are identified, generating a connectome map. +1. Analysis can then be performed on the map to examine and explore the +connectome of interest. + +### **Full documentation:** [here](https://scattr.readthedocs.io/en/stable/) + +## Relevant Papers + +* Kai, J., Khan, A.R., Haast, R.A.M., Lau, J.C. (2022). +Mapping the subcortical connectome using in vivo diffusion MRI: feasibility +and reliability. Terra incognita: diving into the human subcortex, +special issue of NeuroImage. doi: +[10.1016/j.neuroimage.2022.119553](https://doi.org/10.1016/j.neuroimage.2022.119553). diff --git a/scattr.egg-info/SOURCES.txt b/scattr.egg-info/SOURCES.txt new file mode 100644 index 00000000..deef978d --- /dev/null +++ b/scattr.egg-info/SOURCES.txt @@ -0,0 +1,19 @@ +LICENSE +README.md +pyproject.toml +scattr/run.py +scattr.egg-info/PKG-INFO +scattr.egg-info/SOURCES.txt +scattr.egg-info/dependency_links.txt +scattr.egg-info/entry_points.txt +scattr.egg-info/top_level.txt +scattr/workflow/lib/__init__.py +scattr/workflow/lib/utils.py +scattr/workflow/scripts/mrtpipelines/create_exclude_mask.py +scattr/workflow/scripts/mrtpipelines/create_roi_mask.py +scattr/workflow/scripts/qc/registration_qc.py +scattr/workflow/scripts/qc/segmentation_qc.py +scattr/workflow/scripts/zona_bb_subcortex/add_brainstem.py +scattr/workflow/scripts/zona_bb_subcortex/convexHull_roi.py +scattr/workflow/scripts/zona_bb_subcortex/create_seg_mask.py +scattr/workflow/scripts/zona_bb_subcortex/get_num_labels.py \ No newline at end of file diff --git a/scattr.egg-info/dependency_links.txt b/scattr.egg-info/dependency_links.txt new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/scattr.egg-info/dependency_links.txt @@ -0,0 +1 @@ + diff --git a/scattr.egg-info/entry_points.txt b/scattr.egg-info/entry_points.txt new file mode 100644 index 00000000..10190ed6 --- /dev/null +++ b/scattr.egg-info/entry_points.txt @@ -0,0 +1,2 @@ +[console_scripts] +scattr = scattr.run:app.run diff --git a/scattr.egg-info/top_level.txt b/scattr.egg-info/top_level.txt new file mode 100644 index 00000000..c48a46b7 --- /dev/null +++ b/scattr.egg-info/top_level.txt @@ -0,0 +1 @@ +scattr diff --git a/scattr/run.py b/scattr/run.py old mode 100644 new mode 100755 index 0d15d63d..95f2da34 --- a/scattr/run.py +++ b/scattr/run.py @@ -1,23 +1,38 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import os +from pathlib import Path -from snakebids.app import SnakeBidsApp -from snakebids.cli import add_dynamic_args +from snakebids import bidsapp, plugins +try: + from scattr.workflow.lib import utils as utils # Works when run as a package +except ImportError: + from workflow.lib import utils as utils # Works when run directly -def get_parser(): - """Exposes parser for sphinx doc generation, cwd is the docs dir""" - app = SnakeBidsApp("../scattr", skip_parse_args=True) - add_dynamic_args( - app.parser, app.config["parse_args"], app.config["pybids_inputs"] - ) - return app.parser +if "__file__" not in globals(): + __file__ = "../scattr/run.py" + +app = bidsapp.app( + [ + plugins.SnakemakeBidsApp(Path(__file__).resolve().parent), + plugins.BidsValidator(), + plugins.CliConfig("parse_args"), + plugins.ComponentEdit("pybids_inputs"), + ] +) + +# Set the conda prefix directory +conda_prefix = Path(utils.get_download_dir()) / "conda" +# Set the environment variable SNAKEMAKE_CONDA_PREFIX if not already set +if "SNAKEMAKE_CONDA_PREFIX" not in os.environ: + os.environ["SNAKEMAKE_CONDA_PREFIX"] = str(conda_prefix) -def main(): - app = SnakeBidsApp(os.path.abspath(os.path.dirname(__file__))) - app.run_snakemake() + +def get_parser(): + """Exposes parser for sphinx doc generation, cwd is the docs dir""" + return app.build_parser().parser if __name__ == "__main__": - main() + app.run() diff --git a/scattr/workflow/Snakefile b/scattr/workflow/Snakefile index 5b7b1f4d..5c3df45a 100644 --- a/scattr/workflow/Snakefile +++ b/scattr/workflow/Snakefile @@ -5,8 +5,11 @@ from snakebids import ( filter_list, generate_inputs, get_wildcard_constraints, + set_bids_spec, ) +set_bids_spec("v0_0_0") + configfile: "config/snakebids.yml" diff --git a/scattr/workflow/envs/ants.yaml b/scattr/workflow/envs/ants.yaml new file mode 100644 index 00000000..8954ceb7 --- /dev/null +++ b/scattr/workflow/envs/ants.yaml @@ -0,0 +1,9 @@ +--- +name: ants +channels: + - conda-forge + - defaults +dependencies: + - python=3.9 + - ants=2.5.4 + - libitk=5.4.0 \ No newline at end of file diff --git a/scattr/workflow/envs/labelmerge.yaml b/scattr/workflow/envs/labelmerge.yaml new file mode 100644 index 00000000..8790ca00 --- /dev/null +++ b/scattr/workflow/envs/labelmerge.yaml @@ -0,0 +1,9 @@ +--- +name: labelmerge +channels: + - conda-forge +dependencies: + - python=3.11 + - pip + - pip: + - labelmerge==0.4.7 \ No newline at end of file diff --git a/scattr/workflow/envs/mrtrix3.yaml b/scattr/workflow/envs/mrtrix3.yaml new file mode 100644 index 00000000..7358a135 --- /dev/null +++ b/scattr/workflow/envs/mrtrix3.yaml @@ -0,0 +1,4 @@ +--- +name: mrtrix3 +channels: [mrtrix3, conda-forge, defaults] +dependencies: [python=3.11, mrtrix3=3.0.8, numpy] diff --git a/scattr/workflow/envs/neurovis.yaml b/scattr/workflow/envs/neurovis.yaml new file mode 100644 index 00000000..51376355 --- /dev/null +++ b/scattr/workflow/envs/neurovis.yaml @@ -0,0 +1,11 @@ +name: neurovis +channels: + - conda-forge + - defaults +dependencies: + - python=3.9 + - nilearn>=0.10.0,<0.11.0 + - niworkflows>=1.7.9,<2.0.0 + - matplotlib>=3.7.1,<4.0.0 + - numpy>=1.22.3,<2.0.0 + - scipy>=1.8.0,<2.0.0 \ No newline at end of file diff --git a/scattr/workflow/lib/__init__.py b/scattr/workflow/lib/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/scattr/workflow/lib/utils.py b/scattr/workflow/lib/utils.py new file mode 100644 index 00000000..cc4e856c --- /dev/null +++ b/scattr/workflow/lib/utils.py @@ -0,0 +1,13 @@ +import os + +from appdirs import AppDirs + + +def get_download_dir(): + if "SCATTR_CACHE_DIR" in os.environ.keys(): + download_dir = os.environ["SCATTR_CACHE_DIR"] + else: + # create local download dir if it doesn't exist + dirs = AppDirs("scattr", "khanlab") + download_dir = dirs.user_cache_dir + return download_dir diff --git a/scattr/workflow/rules/freesurfer.smk b/scattr/workflow/rules/freesurfer.smk index b2fd5961..c3a0cfd7 100644 --- a/scattr/workflow/rules/freesurfer.smk +++ b/scattr/workflow/rules/freesurfer.smk @@ -109,9 +109,11 @@ rule mgz2nii: NOTE: During conversion, files are renamed to BIDS-esque formatting """ input: - thal=rules.thalamic_segmentation.output.thal_seg - if not config.get("skip_thal_seg") - else [], + thal=( + rules.thalamic_segmentation.output.thal_seg + if not config.get("skip_thal_seg") + else [] + ), aparcaseg=str( Path(bids(root=freesurfer_dir, **inputs.subj_wildcards)).parent / "mri" @@ -141,6 +143,8 @@ rule mgz2nii: "freesurfer" container: config["singularity"]["scattr"] + conda: + "../envs/mrtrix3.yaml" shell: """ export FS_LICENSE={params.fs_license} @@ -180,6 +184,8 @@ rule fs_xfm_to_native: "freesurfer" container: config["singularity"]["scattr"] + conda: + "../envs/ants.yaml" shell: """ antsApplyTransforms -d 3 -n MultiLabel \\ diff --git a/scattr/workflow/rules/mrtpipelines.smk b/scattr/workflow/rules/mrtpipelines.smk index 50d1473e..855846f3 100644 --- a/scattr/workflow/rules/mrtpipelines.smk +++ b/scattr/workflow/rules/mrtpipelines.smk @@ -49,9 +49,11 @@ bids_anat_out = partial( bids_labelmerge = partial( bids, - root=str(Path(labelmerge_dir) / "combined") - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_dir") or zona_dir, + root=( + str(Path(labelmerge_dir) / "combined") + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_dir") or zona_dir + ), **inputs.subj_wildcards, ) @@ -94,6 +96,8 @@ rule dwi2tensor: "dwiproc" container: config["singularity"]["scattr"] + conda: + "../envs/mrtrix3.yaml" shell: """ dwi2tensor -nthreads {threads} -mask {input.mask} \\ diff --git a/scattr/workflow/rules/mrtpipelines/filter_tck.smk b/scattr/workflow/rules/mrtpipelines/filter_tck.smk index ad2f5781..8330b75a 100644 --- a/scattr/workflow/rules/mrtpipelines/filter_tck.smk +++ b/scattr/workflow/rules/mrtpipelines/filter_tck.smk @@ -140,23 +140,29 @@ rule filter_combine_tck: threads: 1 resources: tmp_dir=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), **wildcards, ), tmp_combined_tck=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="filteredsubcortical", suffix="tractography.tck", **wildcards, ), tmp_combined_weights=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="filteredsubcortical", suffix="tckWeights.txt", **wildcards, @@ -169,6 +175,8 @@ rule filter_combine_tck: "tractography_update" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ mkdir -p {resources.tmp_dir} @@ -214,23 +222,29 @@ rule filtered_tck2connectome: threads: 32 resources: tmp_dir=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), **wildcards, ), tmp_sl_assignment=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="filteredsubcortical", suffix="nodeAssignment.txt", **wildcards, ), tmp_node_weights=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="filteredsubcortical", suffix="nodeWeights.csv", **wildcards, @@ -243,6 +257,8 @@ rule filtered_tck2connectome: "tractography_update" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """mkdir -p {resources.tmp_dir} diff --git a/scattr/workflow/rules/mrtpipelines/preproc.smk b/scattr/workflow/rules/mrtpipelines/preproc.smk index f3da513c..ddcc95a7 100644 --- a/scattr/workflow/rules/mrtpipelines/preproc.smk +++ b/scattr/workflow/rules/mrtpipelines/preproc.smk @@ -9,14 +9,14 @@ rule nii2mif: root=mrtrix_dir, datatype="dwi", suffix="dwi.mif", - **inputs.subj_wildcards + **inputs.subj_wildcards, ), mask=bids( root=mrtrix_dir, datatype="dwi", desc="brain", suffix="mask.mif", - **inputs.subj_wildcards + **inputs.subj_wildcards, ), threads: 4 resources: @@ -28,6 +28,8 @@ rule nii2mif: "dwiproc" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ mrconvert -nthreads {threads} -fslgrad {input.bvec} {input.bval} \\ @@ -76,6 +78,8 @@ rule dwi2response: "dwiproc" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ echo 'BZeroThreshold: {params.bzero_thresh}' > {params.mrtrix_conf} @@ -134,6 +138,8 @@ rule responsemean: "dwiproc_group" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ responsemean {input.subject_rf} {output.avg_rf} \\ @@ -208,6 +214,8 @@ rule dwi2fod: "diffmodel" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ dwi2fod -nthreads {threads} {params.shells} -mask {input.mask} \\ @@ -263,6 +271,8 @@ rule mtnormalise: "diffmodel" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ mtnormalise -nthreads {threads} -mask {input.mask} \\ @@ -296,6 +306,8 @@ rule dwinormalise: bids_log(suffix="dwinormalise.log"), container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" group: "dwiproc" shell: diff --git a/scattr/workflow/rules/mrtpipelines/tractography.smk b/scattr/workflow/rules/mrtpipelines/tractography.smk index da99b24e..b4787ef7 100644 --- a/scattr/workflow/rules/mrtpipelines/tractography.smk +++ b/scattr/workflow/rules/mrtpipelines/tractography.smk @@ -21,15 +21,19 @@ rule tckgen: threads: 32 resources: tmp_dir=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), **wildcards, ), tmp_tck=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="iFOD2", suffix="tractography.tck", **wildcards, @@ -40,6 +44,8 @@ rule tckgen: bids_log(suffix="tckgen.log"), container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ mkdir -p {resources.tmp_dir} @@ -76,6 +82,8 @@ rule tcksift2: bids_log(suffix="tcksift2.log"), container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ tcksift2 -nthreads {threads} -out_mu {output.mu} \\ @@ -100,6 +108,8 @@ checkpoint create_roi_mask: "tract_masks" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" script: "../../scripts/mrtpipelines/create_roi_mask.py" @@ -162,6 +172,8 @@ checkpoint create_exclude_mask: "tract_masks" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" script: "../../scripts/mrtpipelines/create_exclude_mask.py" @@ -195,23 +207,29 @@ rule tck2connectome: threads: 32 resources: tmp_dir=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), **wildcards, ), tmp_sl_assignment=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="subcortical", suffix="nodeAssignment.txt", **wildcards, ), tmp_node_weights=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), desc="subcortical", suffix="nodeWeights.csv", **wildcards, @@ -224,6 +242,8 @@ rule tck2connectome: "tractography_update" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ mkdir -p {resources.tmp_dir} @@ -261,25 +281,31 @@ checkpoint connectome2tck: threads: 32 resources: tmp_dir=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), datatype="unfiltered", **wildcards, ), edge_weight_prefix=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), datatype="unfiltered", desc="subcortical", suffix="tckWeights", **wildcards, ), edge_tck_prefix=lambda wildcards: bids_tractography_out( - root=os.environ.get("SLURM_TMPDIR") - if config.get("slurm_tmpdir") - else "/tmp", + root=( + os.environ.get("SLURM_TMPDIR") + if config.get("slurm_tmpdir") + else "/tmp" + ), datatype="unfiltered", desc="subcortical", suffix="from", @@ -293,6 +319,8 @@ checkpoint connectome2tck: "tractography_update" container: config["singularity"]["scattr"] + conda: + "../../envs/mrtrix3.yaml" shell: """ mkdir -p {resources.tmp_dir} {output.output_dir} diff --git a/scattr/workflow/rules/qc.smk b/scattr/workflow/rules/qc.smk index 46feae66..a77e0376 100644 --- a/scattr/workflow/rules/qc.smk +++ b/scattr/workflow/rules/qc.smk @@ -1,9 +1,11 @@ # BIDS partials bids_labelmerge = partial( bids, - root=str(Path(labelmerge_dir) / "combined") - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_dir") or zona_dir, + root=( + str(Path(labelmerge_dir) / "combined") + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_dir") or zona_dir + ), **inputs.subj_wildcards, ) @@ -21,9 +23,11 @@ rule segment_qc: qc_labels=bids_labelmerge( space="T1w", datatype=None if not config.get("skip_labelmerge") else "anat", - desc="combined" - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_desc"), + desc=( + "combined" + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_desc") + ), suffix="dseg.nii.gz", ), t1w_image=lambda wildcards: inputs["T1w"] @@ -32,9 +36,11 @@ rule segment_qc: output: qc_png=report( bids_qc( - desc="labelmerge" - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_desc"), + desc=( + "labelmerge" + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_desc") + ), suffix="dsegQC.png", ), caption="../report/dseg_qc.rst", @@ -43,9 +49,11 @@ rule segment_qc: ), qc_html=report( bids_qc( - desc="labelmerge" - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_desc"), + desc=( + "labelmerge" + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_desc") + ), suffix="dsegQC.html", ), category="Label Segmentation QC", @@ -59,6 +67,8 @@ rule segment_qc: "qc" container: config["singularity"]["scattr"] + conda: + "../envs/neurovis.yaml" script: "../scripts/qc/segmentation_qc.py" @@ -97,6 +107,8 @@ rule registration_qc: "qc" container: config["singularity"]["scattr"] + conda: + "../envs/neurovis.yaml" script: "../scripts/qc/registration_qc.py" diff --git a/scattr/workflow/rules/zona_bb_subcortex.smk b/scattr/workflow/rules/zona_bb_subcortex.smk index 68a7b487..75c83962 100644 --- a/scattr/workflow/rules/zona_bb_subcortex.smk +++ b/scattr/workflow/rules/zona_bb_subcortex.smk @@ -17,9 +17,11 @@ bids_anat = partial( bids_labelmerge = partial( bids, - root=str(Path(labelmerge_dir) / "combined") - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_dir") or zona_dir, + root=( + str(Path(labelmerge_dir) / "combined") + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_dir") or zona_dir + ), **inputs.subj_wildcards, ) @@ -100,6 +102,8 @@ rule reg2native: "subcortical_1" container: config["singularity"]["scattr"] + conda: + "../envs/ants.yaml" shell: """ echo {input.target} @@ -140,6 +144,8 @@ rule warp2native: "subcortical_1" container: config["singularity"]["scattr"] + conda: + "../envs/ants.yaml" shell: """ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} @@ -153,22 +159,30 @@ rule warp2native: rule labelmerge: input: - zona_seg=inputs["T1w"].expand( - rules.warp2native.output.nii, allow_missing=True - ) - if not config.get("labelmerge_base_dir") - else [], - fs_seg=inputs["T1w"].expand( - rules.fs_xfm_to_native.output.thal, allow_missing=True - ) - if not config.get("labelmerge_overlay_dir") - else [], - fs_tsv=rules.cp_fs_tsv.output.fs_tsv - if not config.get("labelmerge_overlay_dir") - else [], - zona_tsv=rules.cp_zona_tsv.output.zona_tsv - if not config.get("labelmerge_base_dir") - else [], + zona_seg=( + inputs["T1w"].expand( + rules.warp2native.output.nii, allow_missing=True + ) + if not config.get("labelmerge_base_dir") + else [] + ), + fs_seg=( + inputs["T1w"].expand( + rules.fs_xfm_to_native.output.thal, allow_missing=True + ) + if not config.get("labelmerge_overlay_dir") + else [] + ), + fs_tsv=( + rules.cp_fs_tsv.output.fs_tsv + if not config.get("labelmerge_overlay_dir") + else [] + ), + zona_tsv=( + rules.cp_zona_tsv.output.zona_tsv + if not config.get("labelmerge_base_dir") + else [] + ), params: labelmerge_out_dir=directory(labelmerge_dir), labelmerge_base_dir=( @@ -221,6 +235,8 @@ rule labelmerge: "subcortical_group" container: config["singularity"]["scattr"] + conda: + "../envs/labelmerge.yaml" shell: """ labelmerge {params.labelmerge_base_dir} {params.labelmerge_out_dir} \\ @@ -237,9 +253,11 @@ rule get_num_nodes: seg=bids_labelmerge( space="T1w", datatype="anat" if config.get("skip_labelmerge") else "", - desc="combined" - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_desc"), + desc=( + "combined" + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_desc") + ), suffix="dseg.nii.gz", ), output: @@ -247,9 +265,11 @@ rule get_num_nodes: bids_labelmerge( space="T1w", datatype="anat" if config.get("skip_labelmerge") else "", - desc="combined" - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_desc"), + desc=( + "combined" + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_desc") + ), suffix="numNodes.txt", ) ), @@ -261,6 +281,8 @@ rule get_num_nodes: "subcortical_2" container: config["singularity"]["scattr"] + conda: + "../envs/neurovis.yaml" script: "../scripts/zona_bb_subcortex/get_num_labels.py" @@ -271,9 +293,11 @@ rule binarize: output: mask=bids_labelmerge( space="T1w", - desc="combined" - if not config.get("skip_labelmerge") - else config.get("labelmerge_base_desc"), + desc=( + "combined" + if not config.get("skip_labelmerge") + else config.get("labelmerge_base_desc") + ), suffix="mask.nii.gz", ), threads: 4 @@ -286,6 +310,8 @@ rule binarize: "subcortical_2" container: config["singularity"]["scattr"] + conda: + "../envs/neurovis.yaml" script: "../scripts/zona_bb_subcortex/create_seg_mask.py" @@ -293,9 +319,11 @@ rule binarize: rule add_brainstem: input: mask=rules.binarize.output.mask, - aparcaseg=rules.fs_xfm_to_native.output.aparcaseg - if not config.get("skip_brainstem") - else [], + aparcaseg=( + rules.fs_xfm_to_native.output.aparcaseg + if not config.get("skip_brainstem") + else [] + ), output: mask=bids_labelmerge( space="T1w", @@ -312,15 +340,19 @@ rule add_brainstem: "subcortical_2" container: config["singularity"]["scattr"] + conda: + "../envs/neurovis.yaml" script: "../scripts/zona_bb_subcortex/add_brainstem.py" rule create_convex_hull: input: - bin_seg=rules.binarize.output.mask - if config["skip_brainstem"] - else rules.add_brainstem.output.mask, + bin_seg=( + rules.binarize.output.mask + if config["skip_brainstem"] + else rules.add_brainstem.output.mask + ), output: convex_hull=bids_labelmerge( space="T1w", @@ -337,5 +369,7 @@ rule create_convex_hull: "subcortical_2" container: config["singularity"]["scattr"] + conda: + "../envs/neurovis.yaml" script: "../scripts/zona_bb_subcortex/convexHull_roi.py" diff --git a/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py b/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py index 7f562bbc..a408e93a 100644 --- a/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py +++ b/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py @@ -32,10 +32,7 @@ def create_roi_mask( **wildcards, ) - shell( - "mrcalc -nthreads {threads} " - "{subcortical_seg} {idx} -eq {roi} -force" - ) + shell("mrcalc -nthreads {threads} " "{subcortical_seg} {idx} -eq {roi} -force") # Build mask list and create in parallel # label_list = [idx for idx in range(1, num_labels+1)] diff --git a/scattr/workflow/scripts/qc/registration_qc.py b/scattr/workflow/scripts/qc/registration_qc.py index e6b05807..4be4a884 100644 --- a/scattr/workflow/scripts/qc/registration_qc.py +++ b/scattr/workflow/scripts/qc/registration_qc.py @@ -2,11 +2,7 @@ import matplotlib from nilearn.image import load_img from nilearn.plotting import view_img -from niworkflows.viz.utils import ( - compose_view, - cuts_from_bbox, - plot_registration, -) +from niworkflows.viz.utils import compose_view, cuts_from_bbox, plot_registration def registration_qc( diff --git a/scattr/workflow/scripts/zona_bb_subcortex/add_brainstem.py b/scattr/workflow/scripts/zona_bb_subcortex/add_brainstem.py index 9ffda266..4bf0629f 100644 --- a/scattr/workflow/scripts/zona_bb_subcortex/add_brainstem.py +++ b/scattr/workflow/scripts/zona_bb_subcortex/add_brainstem.py @@ -7,9 +7,7 @@ def add_brainstem(dseg_mask, aparcaseg, out_mask): aparcaseg_data = nib.load(aparcaseg) affine, header = aparcaseg_data.affine, aparcaseg_data.header - out_data = (aparcaseg_data.get_fdata() == 16) | ( - dseg_mask_data.get_fdata() > 0 - ) + out_data = (aparcaseg_data.get_fdata() == 16) | (dseg_mask_data.get_fdata() > 0) out_nii = nib.Nifti1Image(dataobj=out_data, affine=affine, header=header) nib.save(out_nii, out_mask)