diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..1557666 --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,39 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Python package + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.7', '3.8'] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --builtins=snakemake + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --builtins=snakemake + - name: Test with pytest + run: | + pytest diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml new file mode 100644 index 0000000..4e1ef42 --- /dev/null +++ b/.github/workflows/python-publish.yml @@ -0,0 +1,31 @@ +# This workflows will upload a Python Package using Twine when a release is created +# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries + +name: Upload Python Package + +on: + release: + types: [created] + +jobs: + deploy: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.x' + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install setuptools wheel twine + - name: Build and publish + env: + TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} + TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + run: | + python setup.py sdist bdist_wheel + twine upload dist/* diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..93c4d25 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,3 @@ +recursive-include denoise_fmri/resources * +recursive-include denoise_fmri/config * +recursive-include denoise_fmri/workflow * diff --git a/README.md b/README.rst similarity index 80% rename from README.md rename to README.rst index 616cf81..48b8a90 100644 --- a/README.md +++ b/README.rst @@ -1,4 +1,5 @@ -# snakebids app for denoising fmriprep output +denoise-fmri +============ Known issues: - pybids has an incompatibility with the latest fmriprep (20.2.0) dataset_description.json, need to replace this with the version in resources/dataset_description.json for now diff --git a/denoise_fmri/__init__.py b/denoise_fmri/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/denoise_fmri/__pycache__/__init__.cpython-38.pyc b/denoise_fmri/__pycache__/__init__.cpython-38.pyc new file mode 100644 index 0000000..fac6637 Binary files /dev/null and b/denoise_fmri/__pycache__/__init__.cpython-38.pyc differ diff --git a/denoise_fmri/__pycache__/run.cpython-38.pyc b/denoise_fmri/__pycache__/run.cpython-38.pyc new file mode 100644 index 0000000..c9f8292 Binary files /dev/null and b/denoise_fmri/__pycache__/run.cpython-38.pyc differ diff --git a/config/snakebids.yml b/denoise_fmri/config/snakebids.yml similarity index 100% rename from config/snakebids.yml rename to denoise_fmri/config/snakebids.yml diff --git a/denoise_fmri/pipeline_description.json b/denoise_fmri/pipeline_description.json new file mode 100644 index 0000000..83bd4fe --- /dev/null +++ b/denoise_fmri/pipeline_description.json @@ -0,0 +1,15 @@ +{ + "Name": "denoise_fmri - BIDS app for denoising fmriprep outputs", + "BIDSVersion": "1.4.0", + "DatasetType": "derivative", + "GeneratedBy": [ + { + "Name": "denoise_fmri", + "Version": "0.1.0", + "CodeURL": "http://github.com/akhanf/denoise-fmri", + "Author": "Ali Khan", + "AuthorEmail": "ali.khan@uwo.ca" + + } + ] +} diff --git a/resources/dataset_description.json b/denoise_fmri/resources/dataset_description.json similarity index 100% rename from resources/dataset_description.json rename to denoise_fmri/resources/dataset_description.json diff --git a/run.py b/denoise_fmri/run.py similarity index 55% rename from run.py rename to denoise_fmri/run.py index 8dc200e..3cb5914 100755 --- a/run.py +++ b/denoise_fmri/run.py @@ -3,8 +3,13 @@ from snakebids.app import SnakeBidsApp -def main(): +def get_parser(): + """Exposes parser for sphinx doc generation, cwd is the docs dir""" + app = SnakeBidsApp('../denoise_fmri',skip_parse_args=True) + return app.parser + +def main(): app = SnakeBidsApp(os.path.abspath(os.path.dirname(__file__))) app.run_snakemake() diff --git a/workflow/Snakefile b/denoise_fmri/workflow/Snakefile similarity index 100% rename from workflow/Snakefile rename to denoise_fmri/workflow/Snakefile diff --git a/workflow/scripts/denoise.py b/denoise_fmri/workflow/scripts/denoise.py similarity index 100% rename from workflow/scripts/denoise.py rename to denoise_fmri/workflow/scripts/denoise.py diff --git a/workflow/scripts/smooth.py b/denoise_fmri/workflow/scripts/smooth.py similarity index 100% rename from workflow/scripts/smooth.py rename to denoise_fmri/workflow/scripts/smooth.py diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..e35d885 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1 @@ +_build diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..06ef387 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,63 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +# import os +# import sys +# sys.path.insert(0, os.path.abspath('.')) +import sphinx_rtd_theme + + +# -- Project information ----------------------------------------------------- + + +project = 'app_name' +copyright = '2020, Authors here' +author = 'Authors here' + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx_rtd_theme", + "sphinxarg.ext", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + + +master_doc = 'index' + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + + + + diff --git a/docs/getting_started/installation.rst b/docs/getting_started/installation.rst new file mode 100644 index 0000000..5cda299 --- /dev/null +++ b/docs/getting_started/installation.rst @@ -0,0 +1,56 @@ +Installation +============ + +Template snakebids BIDS App + + +Requirements +------------ + +Docker (Mac/Windows/Linux) or Singularity (Linux) + +Docker: +^^^^^^^ + +Pull the container: + +.. code-block:: + + docker pull khanlab/app_name:latest + +do a dry run, printing the command at each step: + +.. code-block:: + + docker run -it --rm -v PATH_TO_BIDS_DIR:/bids:ro -v PATH_TO_OUTPUT_DIR:/output khanlab/app_name:latest /bids /output participant -np + +run it with maximum number of cores: + +.. code-block:: + + docker run -it --rm -v PATH_TO_BIDS_DIR:/bids:ro -v PATH_TO_OUTPUT_DIR:/output khanlab/app_name:latest /bids /output participant -p --cores all + + +Singularity: +^^^^^^^^^^^^ + +Pull the container: + +.. code-block:: + + singularity pull khanlab_app_name_latest.sif docker://khanlab/app_name:latest + +do a dry run, printing the command at each step: + +.. code-block:: + + singularity run -e khanlab_app_name_latest.sif khanlab/app_name:latest PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant -np + +run it with maximum number of cores: + +.. code-block:: + + singularity run -e khanlab_app_name_latest.sif khanlab/app_name:latest PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant -p --cores all + + + diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..4377f08 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,32 @@ +.. hippunfold documentation master file, created by + sphinx-quickstart on Thu Jul 30 10:15:34 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +.. include:: ../README.rst + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + +.. toctree:: + :caption: Getting started + :name: getting_started + :hidden: + :maxdepth: 1 + + getting_started/installation + +.. toctree:: + :caption: Usage + :name: usage + :hidden: + :maxdepth: 1 + + usage/app_cli + usage/snakemake_cli + + + + diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..17115ac --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,3 @@ +sphinx-argparse +sphinx_rtd_theme +snakebids==0.2.0 diff --git a/docs/usage/app_cli.rst b/docs/usage/app_cli.rst new file mode 100644 index 0000000..31ba495 --- /dev/null +++ b/docs/usage/app_cli.rst @@ -0,0 +1,9 @@ +Command line interface +-------------------- + +.. argparse:: + :filename: ../app_name/run.py + :func: get_parser + :prog: hippunfold + + diff --git a/docs/usage/snakemake_cli.rst b/docs/usage/snakemake_cli.rst new file mode 100644 index 0000000..f8261fb --- /dev/null +++ b/docs/usage/snakemake_cli.rst @@ -0,0 +1,9 @@ +Snakemake Command line interface +________________________________ + +.. argparse:: + :module: snakemake + :func: get_argument_parser + :prog: snakemake + + diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..729790b --- /dev/null +++ b/requirements.txt @@ -0,0 +1,48 @@ +amply==0.1.4 +appdirs==1.4.4 +attrs==20.3.0 +bids-validator==1.5.8 +certifi==2020.12.5 +chardet==3.0.4 +click==7.1.2 +ConfigArgParse==1.2.3 +datrie==0.8.2 +docopt==0.6.2 +docutils==0.16 +gitdb==4.0.5 +GitPython==3.1.11 +idna==2.10 +ipython-genutils==0.2.0 +joblib==1.0.0 +jsonschema==3.2.0 +jupyter-core==4.7.0 +nbformat==5.0.8 +nibabel==3.2.1 +nilearn==0.7.0 +num2words==0.5.10 +numpy==1.19.4 +packaging==20.8 +pandas==1.1.5 +patsy==0.5.1 +psutil==5.7.3 +PuLP==2.3.1 +pybids==0.12.3 +pyparsing==2.4.7 +pyrsistent==0.17.3 +python-dateutil==2.8.1 +pytz==2020.4 +PyYAML==5.3.1 +ratelimiter==1.2.0.post0 +requests==2.25.0 +scikit-learn==0.23.2 +scipy==1.5.4 +six==1.15.0 +smmap==3.0.4 +snakebids==0.2.0 +snakemake==5.30.1 +SQLAlchemy==1.3.20 +threadpoolctl==2.1.0 +toposort==1.5 +traitlets==5.0.5 +urllib3==1.26.2 +wrapt==1.12.1 diff --git a/setup.py b/setup.py index 64c6ad6..73994c6 100644 --- a/setup.py +++ b/setup.py @@ -1,28 +1,40 @@ import setuptools +import json -with open("README.md", "r") as fh: +with open("README.rst", "r") as fh: long_description = fh.read() +with open('denoise_fmri/pipeline_description.json', 'r') as fh: + pipeline = json.load(fh) + name = pipeline['GeneratedBy'][0]['Name'] + description = pipeline['Name'] + version = pipeline['GeneratedBy'][0]['Version'] + url = pipeline['GeneratedBy'][0]['CodeURL'] + author = pipeline['GeneratedBy'][0]['Author'] + author_email = pipeline['GeneratedBy'][0]['AuthorEmail'] + setuptools.setup( - name="denoise-fmri", - version="0.1.0", - author="Ali Khan", - author_email="alik@robarts.ca", - description="Snakemake BIDS app for denoising fmriprep, uses the snakebids package for running snakemake workflow as bids app", + name=name, + version=version, + author=author, + author_email=author_email, + description=description, long_description=long_description, - long_description_content_type="text/markdown", - url="https://github.com/akhanf/denoise-fmri", + long_description_content_type="text/x-rst", + url=url, packages=setuptools.find_packages(), + include_package_data=True, classifiers=[ "Programming Language :: Python :: 3", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", ], entry_points={'console_scripts': [ - 'denoise-fmri=run:main' + 'denoise_fmri=denoise_fmri.run:main' ]}, install_requires=[ - "snakebids>=0.1.1", + "snakebids>=0.2.0", + "snakemake>=5.28.0", "nilearn", "pandas", "numpy" diff --git a/tests/bids_01/dataset_description.json b/tests/bids_01/dataset_description.json new file mode 100644 index 0000000..7535086 --- /dev/null +++ b/tests/bids_01/dataset_description.json @@ -0,0 +1,23 @@ +{ + "Acknowledgements": "TODO: whom you want to acknowledge", + "Authors": [ + "TODO:", + "First1 Last1", + "First2 Last2", + "..." + ], + "BIDSVersion": "1.0.1", + "DatasetDOI": "TODO: eventually a DOI for the dataset", + "Funding": [ + "TODO", + "GRANT #1", + "GRANT #2" + ], + "HowToAcknowledge": "TODO: describe how to acknowledge -- either cite a corresponding paper, or just in acknowledgement section", + "License": "TODO: choose a license, e.g. PDDL (http://opendatacommons.org/licenses/pddl/)", + "Name": "TODO: name of the dataset", + "ReferencesAndLinks": [ + "TODO", + "List of papers or websites" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/dataset_description.json b/tests/bids_01/derivatives/fmriprep/dataset_description.json new file mode 100644 index 0000000..7537e56 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/dataset_description.json @@ -0,0 +1,24 @@ +{ + "Name": "fMRIPrep - fMRI PREProcessing workflow", + "BIDSVersion": "1.4.0", + "DatasetType": "derivative", + "PipelineDescription": { + "Name": "fMRIPrep", + "Version": "20.2.0" + }, + "GeneratedBy": [ + { + "Name": "fMRIPrep", + "Version": "20.2.0", + "CodeURL": "https://github.com/poldracklab/fmriprep/archive/20.2.0.tar.gz" + } + ], + "HowToAcknowledge": "Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4), and include the generated citation boilerplate within the Methods section of the text.", + "SourceDatasets": [ + { + "URL": "https://doi.org/TODO: eventually a DOI for the dataset", + "DOI": "TODO: eventually a DOI for the dataset" + } + ], + "License": "TODO: choose a license, e.g. PDDL (http://opendatacommons.org/licenses/pddl/)" +} diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-brain_mask.json new file mode 100644 index 0000000..f0fee1c --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-brain_mask.json @@ -0,0 +1,6 @@ +{ + "RawSources": [ + "sub-0001/anat/sub-0001_acq-MPRAGE_run-01_T1w.nii.gz" + ], + "Type": "Brain" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-preproc_T1w.json b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-preproc_T1w.json new file mode 100644 index 0000000..0b295ff --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-preproc_T1w.json @@ -0,0 +1,3 @@ +{ + "SkullStripped": false +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-preproc_T1w.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_desc-preproc_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_dseg.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_dseg.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5 b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5 new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_label-CSF_probseg.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_label-CSF_probseg.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_label-GM_probseg.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_label-GM_probseg.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_label-WM_probseg.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_label-WM_probseg.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json new file mode 100644 index 0000000..2a12826 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json @@ -0,0 +1,4 @@ +{ + "RawSources": "tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz", + "Type": "Brain" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.json b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.json new file mode 100644 index 0000000..2dc471a --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.json @@ -0,0 +1,4 @@ +{ + "SkullStripped": true, + "keep_dtype": true +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/anat/sub-0001_acq-MPRAGE_run-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz 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a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_desc-confounds_timeseries.tsv b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_desc-confounds_timeseries.tsv new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_from-T1w_to-scanner_mode-image_xfm.txt b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_from-T1w_to-scanner_mode-image_xfm.txt new file mode 100644 index 0000000..25e01a4 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_from-T1w_to-scanner_mode-image_xfm.txt @@ -0,0 +1,5 @@ +#Insight Transform File V1.0 +#Transform 0 +Transform: MatrixOffsetTransformBase_double_3_3 +Parameters: 0.9999765351499204 0.0028101577852398052 -0.005000231795505298 -0.002880868517298168 0.9998906342717938 -0.014498232315781345 0.004958560329036282 0.014512402506233979 0.9998823862696186 -0.43771575966346177 -1.5286706356724409 -0.830129711704501 +FixedParameters: 0 0 0 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_from-scanner_to-T1w_mode-image_xfm.txt b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_from-scanner_to-T1w_mode-image_xfm.txt new file mode 100644 index 0000000..04b4400 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_from-scanner_to-T1w_mode-image_xfm.txt @@ -0,0 +1,5 @@ +#Insight Transform File V1.0 +#Transform 0 +Transform: MatrixOffsetTransformBase_double_3_3 +Parameters: 0.9999905713742028 -0.0028824132126515946 0.004958977996965715 0.0028086593453420117 0.9998908512053835 0.014512400603812814 -0.00499986201777021 -0.014498231039881265 0.9998824006888478 0.43742196318363824 1.541780344208476 0.8056805438085632 +FixedParameters: 0 0 0 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json new file mode 100644 index 0000000..d009d26 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json @@ -0,0 +1,5 @@ +{ + "RawSources": [ + "sub-0001/func/sub-0001_task-movie_run-01_bold.nii.gz" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json new file mode 100644 index 0000000..cca129f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json @@ -0,0 +1,5 @@ +{ + "RepetitionTime": 1.25, + "SkullStripped": false, + "TaskName": "movie" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_boldref.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_boldref.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-brain_mask.json new file mode 100644 index 0000000..d009d26 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-brain_mask.json @@ -0,0 +1,5 @@ +{ + "RawSources": [ + "sub-0001/func/sub-0001_task-movie_run-01_bold.nii.gz" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-preproc_bold.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-preproc_bold.json new file mode 100644 index 0000000..cca129f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-preproc_bold.json @@ -0,0 +1,5 @@ +{ + "RepetitionTime": 1.25, + "SkullStripped": false, + "TaskName": "movie" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_boldref.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_boldref.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-brain_mask.json new file mode 100644 index 0000000..d009d26 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-brain_mask.json @@ -0,0 +1,5 @@ +{ + "RawSources": [ + "sub-0001/func/sub-0001_task-movie_run-01_bold.nii.gz" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-preproc_bold.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-preproc_bold.json new file mode 100644 index 0000000..cca129f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-preproc_bold.json @@ -0,0 +1,5 @@ +{ + "RepetitionTime": 1.25, + "SkullStripped": false, + "TaskName": "movie" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-preproc_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-movie_run-1_space-T1w_desc-preproc_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_AROMAnoiseICs.csv b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_AROMAnoiseICs.csv new file mode 100644 index 0000000..b52d13f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_AROMAnoiseICs.csv @@ -0,0 +1 @@ +1,2,3,4,6,7,9,14,17,18,22,24,33,34,38,40,41,43,44,48,49,51,52,54,56,57,58,59,61,62,63,67,68,70,73,75,79,80,82,85 \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-MELODIC_mixing.tsv b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-MELODIC_mixing.tsv new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-confounds_timeseries.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-confounds_timeseries.json new file mode 100644 index 0000000..190b869 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-confounds_timeseries.json @@ -0,0 +1,10394 @@ +{ + "a_comp_cor_00": { + "CumulativeVarianceExplained": 0.1199142674, + "Mask": "CSF", + "Method": "aCompCor", + "Retained": true, + "SingularValue": 246.5403493301, + "VarianceExplained": 0.1199142674 + }, + "a_comp_cor_01": { + "CumulativeVarianceExplained": 0.2153994186, + "Mask": "CSF", + "Method": 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"t_comp_cor_04": { + "CumulativeVarianceExplained": 0.4456961774, + "Method": "tCompCor", + "Retained": true, + "SingularValue": 140.5854937492, + "VarianceExplained": 0.0254547388 + }, + "t_comp_cor_05": { + "CumulativeVarianceExplained": 0.469753562, + "Method": "tCompCor", + "Retained": true, + "SingularValue": 136.6722652856, + "VarianceExplained": 0.0240573845 + }, + "t_comp_cor_06": { + "CumulativeVarianceExplained": 0.4891284828, + "Method": "tCompCor", + "Retained": true, + "SingularValue": 122.6524297904, + "VarianceExplained": 0.0193749208 + }, + "t_comp_cor_07": { + "CumulativeVarianceExplained": 0.5064372901, + "Method": "tCompCor", + "Retained": true, + "SingularValue": 115.9283780811, + "VarianceExplained": 0.0173088073 + }, + "tcompcor": { + "Method": "Mean" + }, + "white_matter": { + "Method": "Mean" + } +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-confounds_timeseries.tsv b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_desc-confounds_timeseries.tsv new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_from-T1w_to-scanner_mode-image_xfm.txt b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_from-T1w_to-scanner_mode-image_xfm.txt new file mode 100644 index 0000000..91a1042 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_from-T1w_to-scanner_mode-image_xfm.txt @@ -0,0 +1,5 @@ +#Insight Transform File V1.0 +#Transform 0 +Transform: MatrixOffsetTransformBase_double_3_3 +Parameters: 0.9999785939712378 0.0020329570236757976 -0.00496003441851604 -0.0020700056184853426 0.9999674755838814 -0.00778405704385976 0.004943655893898322 0.007794203503531938 0.9999574529070153 -0.41559342020597967 -1.2798695286176098 -0.2667181246285679 +FixedParameters: 0 0 0 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_from-scanner_to-T1w_mode-image_xfm.txt b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_from-scanner_to-T1w_mode-image_xfm.txt new file mode 100644 index 0000000..52726ad --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_from-scanner_to-T1w_mode-image_xfm.txt @@ -0,0 +1,5 @@ +#Insight Transform File V1.0 +#Transform 0 +Transform: MatrixOffsetTransformBase_double_3_3 +Parameters: 0.9999926758744535 -0.00207154469494057 0.004944083424331273 0.0020314502357896592 0.999967643829983 0.007794212867329481 -0.004959664239258192 -0.00778404148871778 0.9999573537278191 0.41425774324928 1.2827512377762815 0.2546829822242387 +FixedParameters: 0 0 0 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json new file mode 100644 index 0000000..21e3b1f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json @@ -0,0 +1,5 @@ +{ + "RawSources": [ + "sub-0001/func/sub-0001_task-rest_run-01_bold.nii.gz" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json new file mode 100644 index 0000000..a4399b7 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json @@ -0,0 +1,5 @@ +{ + "RepetitionTime": 1.25, + "SkullStripped": false, + "TaskName": "rest" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_boldref.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_boldref.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-brain_mask.json new file mode 100644 index 0000000..21e3b1f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-brain_mask.json @@ -0,0 +1,5 @@ +{ + "RawSources": [ + "sub-0001/func/sub-0001_task-rest_run-01_bold.nii.gz" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-preproc_bold.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-preproc_bold.json new file mode 100644 index 0000000..a4399b7 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-preproc_bold.json @@ -0,0 +1,5 @@ +{ + "RepetitionTime": 1.25, + "SkullStripped": false, + "TaskName": "rest" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_boldref.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_boldref.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-brain_mask.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-brain_mask.json new file mode 100644 index 0000000..21e3b1f --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-brain_mask.json @@ -0,0 +1,5 @@ +{ + "RawSources": [ + "sub-0001/func/sub-0001_task-rest_run-01_bold.nii.gz" + ] +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-brain_mask.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-brain_mask.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-preproc_bold.json b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-preproc_bold.json new file mode 100644 index 0000000..a4399b7 --- /dev/null +++ b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-preproc_bold.json @@ -0,0 +1,5 @@ +{ + "RepetitionTime": 1.25, + "SkullStripped": false, + "TaskName": "rest" +} \ No newline at end of file diff --git a/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz b/tests/bids_01/derivatives/fmriprep/sub-0001/func/sub-0001_task-rest_run-1_space-T1w_desc-preproc_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/sub-0001/anat/sub-0001_acq-MPRAGE_run-01_T1w.json b/tests/bids_01/sub-0001/anat/sub-0001_acq-MPRAGE_run-01_T1w.json new file mode 100644 index 0000000..52f7566 --- /dev/null +++ b/tests/bids_01/sub-0001/anat/sub-0001_acq-MPRAGE_run-01_T1w.json @@ -0,0 +1,741 @@ +{ + "AcquisitionMatrixPE": 310, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:43:23.132500", + "BaseResolution": 320, + "BodyPartExamined": "BRAIN", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20190720 GCC5.4.0", + "DeviceSerialNumber": "67007", + "DwellTime": 7.4e-06, + "EchoTime": 0.00228, + "FlipAngle": 8, + 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at end of file diff --git a/tests/bids_01/sub-0001/func/sub-0001_task-movie_run-01_bold.nii.gz b/tests/bids_01/sub-0001/func/sub-0001_task-movie_run-01_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/bids_01/sub-0001/func/sub-0001_task-movie_run-01_events.tsv b/tests/bids_01/sub-0001/func/sub-0001_task-movie_run-01_events.tsv new file mode 100644 index 0000000..2025bd3 --- /dev/null +++ b/tests/bids_01/sub-0001/func/sub-0001_task-movie_run-01_events.tsv @@ -0,0 +1 @@ +onset duration trial_type response_time stim_file diff --git a/tests/bids_01/sub-0001/func/sub-0001_task-rest_run-01_bold.json b/tests/bids_01/sub-0001/func/sub-0001_task-rest_run-01_bold.json new file mode 100644 index 0000000..94e68d2 --- /dev/null +++ b/tests/bids_01/sub-0001/func/sub-0001_task-rest_run-01_bold.json @@ -0,0 +1,178 @@ +{ + "AcquisitionMatrixPE": 88, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:17:9.312500", + "BandwidthPerPixelPhaseEncode": 34.965, + "BaseResolution": 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subprocess.check_call(['./denoise_fmri/run.py','tests/bids_01','tests/out_01','participant','-np'])