fmriprep


Namefmriprep JSON
Version 23.2.1 PyPI version JSON
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SummaryA robust and easy-to-use pipeline for preprocessing of diverse fMRI data
upload_time2024-03-06 17:35:48
maintainer
docs_urlNone
author
requires_python>=3.10
licenseApache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright 2020 The NiPreps Developers Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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            Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize
the data before statistical analysis.
Generally, researchers create ad hoc preprocessing workflows for each dataset,
building upon a large inventory of available tools.
The complexity of these workflows has snowballed with rapid advances in
acquisition and processing.
fMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and
reproducible preprocessing for task-based and resting fMRI data.
fMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of
virtually any dataset, ensuring high-quality preprocessing without manual intervention.
fMRIPrep robustly produces high-quality results on diverse fMRI data.
Additionally, fMRIPrep introduces less uncontrolled spatial smoothness than observed
with commonly used preprocessing tools.
fMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing
workflow, which can help ensure the validity of inference and the interpretability
of results.

The workflow is based on `Nipype <https://nipype.readthedocs.io>`_ and encompasses a large
set of tools from well-known neuroimaging packages, including
`FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_,
`ANTs <https://stnava.github.io/ANTs/>`_,
`FreeSurfer <https://surfer.nmr.mgh.harvard.edu/>`_,
`AFNI <https://afni.nimh.nih.gov/>`_,
and `Nilearn <https://nilearn.github.io/>`_.
This pipeline was designed to provide the best software implementation for each state of
preprocessing, and will be updated as newer and better neuroimaging software becomes
available.

fMRIPrep performs basic preprocessing steps (coregistration, normalization, unwarping, noise
component extraction, segmentation, skullstripping etc.) providing outputs that can be
easily submitted to a variety of group level analyses, including task-based or resting-state
fMRI, graph theory measures, surface or volume-based statistics, etc.
fMRIPrep allows you to easily do the following:

  * Take fMRI data from *unprocessed* (only reconstructed) to ready for analysis.
  * Implement tools from different software packages.
  * Achieve optimal data processing quality by using the best tools available.
  * Generate preprocessing-assessment reports, with which the user can easily identify problems.
  * Receive verbose output concerning the stage of preprocessing for each subject, including
    meaningful errors.
  * Automate and parallelize processing steps, which provides a significant speed-up from
    typical linear, manual processing.

[Nat Meth doi:`10.1038/s41592-018-0235-4 <https://doi.org/10.1038/s41592-018-0235-4>`_]
[Documentation `fmriprep.org <https://fmriprep.readthedocs.io>`_]
[Software doi:`10.5281/zenodo.852659 <https://doi.org/10.5281/zenodo.852659>`_]
[Support `neurostars.org <https://neurostars.org/tags/fmriprep>`_]

License information
-------------------
*fMRIPrep* adheres to the
`general licensing guidelines <https://www.nipreps.org/community/licensing/>`__
of the *NiPreps framework*.

License
~~~~~~~
Copyright (c) 2023, the *NiPreps* Developers.

As of the 21.0.x pre-release and release series, *fMRIPrep* is
licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
`http://www.apache.org/licenses/LICENSE-2.0
<http://www.apache.org/licenses/LICENSE-2.0>`__.

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

            

Raw data

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    "description": "Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize\nthe data before statistical analysis.\nGenerally, researchers create ad hoc preprocessing workflows for each dataset,\nbuilding upon a large inventory of available tools.\nThe complexity of these workflows has snowballed with rapid advances in\nacquisition and processing.\nfMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and\nreproducible preprocessing for task-based and resting fMRI data.\nfMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of\nvirtually any dataset, ensuring high-quality preprocessing without manual intervention.\nfMRIPrep robustly produces high-quality results on diverse fMRI data.\nAdditionally, fMRIPrep introduces less uncontrolled spatial smoothness than observed\nwith commonly used preprocessing tools.\nfMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing\nworkflow, which can help ensure the validity of inference and the interpretability\nof results.\n\nThe workflow is based on `Nipype <https://nipype.readthedocs.io>`_ and encompasses a large\nset of tools from well-known neuroimaging packages, including\n`FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_,\n`ANTs <https://stnava.github.io/ANTs/>`_,\n`FreeSurfer <https://surfer.nmr.mgh.harvard.edu/>`_,\n`AFNI <https://afni.nimh.nih.gov/>`_,\nand `Nilearn <https://nilearn.github.io/>`_.\nThis pipeline was designed to provide the best software implementation for each state of\npreprocessing, and will be updated as newer and better neuroimaging software becomes\navailable.\n\nfMRIPrep performs basic preprocessing steps (coregistration, normalization, unwarping, noise\ncomponent extraction, segmentation, skullstripping etc.) providing outputs that can be\neasily submitted to a variety of group level analyses, including task-based or resting-state\nfMRI, graph theory measures, surface or volume-based statistics, etc.\nfMRIPrep allows you to easily do the following:\n\n  * Take fMRI data from *unprocessed* (only reconstructed) to ready for analysis.\n  * Implement tools from different software packages.\n  * Achieve optimal data processing quality by using the best tools available.\n  * Generate preprocessing-assessment reports, with which the user can easily identify problems.\n  * Receive verbose output concerning the stage of preprocessing for each subject, including\n    meaningful errors.\n  * Automate and parallelize processing steps, which provides a significant speed-up from\n    typical linear, manual processing.\n\n[Nat Meth doi:`10.1038/s41592-018-0235-4 <https://doi.org/10.1038/s41592-018-0235-4>`_]\n[Documentation `fmriprep.org <https://fmriprep.readthedocs.io>`_]\n[Software doi:`10.5281/zenodo.852659 <https://doi.org/10.5281/zenodo.852659>`_]\n[Support `neurostars.org <https://neurostars.org/tags/fmriprep>`_]\n\nLicense information\n-------------------\n*fMRIPrep* adheres to the\n`general licensing guidelines <https://www.nipreps.org/community/licensing/>`__\nof the *NiPreps framework*.\n\nLicense\n~~~~~~~\nCopyright (c) 2023, the *NiPreps* Developers.\n\nAs of the 21.0.x pre-release and release series, *fMRIPrep* is\nlicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n`http://www.apache.org/licenses/LICENSE-2.0\n<http://www.apache.org/licenses/LICENSE-2.0>`__.\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n",
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    "license": "Apache License Version 2.0, January 2004 http://www.apache.org/licenses/  TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION  1. Definitions.  \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.  \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.  \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.  \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License.  \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files.  \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types.  \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below).  \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.  \"Contribution\" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, \"submitted\" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as \"Not a Contribution.\"  \"Contributor\" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work.  2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form.  3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed.  4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions:  (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and  (b) You must cause any modified files to carry prominent notices stating that You changed the files; and  (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and  (d) If the Work includes a \"NOTICE\" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.  You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.  5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.  6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file.  7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. 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While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability.  END OF TERMS AND CONDITIONS  APPENDIX: How to apply the Apache License to your work.  To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets \"[]\" replaced with your own identifying information. (Don't include the brackets!)  The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same \"printed page\" as the copyright notice for easier identification within third-party archives.  Copyright 2020 The NiPreps Developers  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ",
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