Merge pull request #3 from mnoergaard/main

Refactor of fMRIPrep to PETPrep

Author: mnoergaard

README.rst

@@ -1,30 +1,30 @@
-*fMRIPrep*: A Robust Preprocessing Pipeline for fMRI Data
+*PETPrep*: A Robust Preprocessing Pipeline for PET Data
 =========================================================
-*fMRIPrep* is a *NiPreps (NeuroImaging PREProcessing toolS)* application
+*PETPrep* is a *NiPreps (NeuroImaging PREProcessing toolS)* application
 (`www.nipreps.org <https://www.nipreps.org>`__) for the preprocessing of
-task-based and resting-state functional MRI (fMRI).
+positron emission tomography (PET) imaging.
 
 .. image:: https://img.shields.io/badge/RRID-SCR__016216-blue.svg
   :target: https://doi.org/10.1038/s41592-018-0235-4
   :alt: RRID:SCR_016216
 
-.. image:: https://img.shields.io/pypi/v/fmriprep.svg
-  :target: https://pypi.python.org/pypi/fmriprep/
+.. image:: https://img.shields.io/pypi/v/petprep.svg
+  :target: https://pypi.python.org/pypi/petprep/
   :alt: Latest Version
 
-.. image:: https://circleci.com/gh/nipreps/fmriprep/tree/master.svg?style=shield
-  :target: https://circleci.com/gh/nipreps/fmriprep/tree/master
+.. image:: https://circleci.com/gh/nipreps/petprep/tree/master.svg?style=shield
+  :target: https://circleci.com/gh/nipreps/petprep/tree/master
 
-.. image:: https://readthedocs.org/projects/fmriprep/badge/?version=latest
-  :target: https://fmriprep.org/en/latest/?badge=latest
+.. image:: https://readthedocs.org/projects/petprep/badge/?version=latest
+  :target: https://petprep.org/en/latest/?badge=latest
   :alt: Documentation Status
 
 .. image:: https://img.shields.io/badge/doi-10.1038%2Fs41592--018--0235--4-blue.svg
   :target: https://doi.org/10.1038/s41592-018-0235-4
   :alt: Published in Nature Methods
 
-.. image:: https://img.shields.io/badge/docker-nipreps/fmriprep-brightgreen.svg?logo=docker&style=flat
-  :target: https://hub.docker.com/r/nipreps/fmriprep/tags/
+.. image:: https://img.shields.io/badge/docker-nipreps/petprep-brightgreen.svg?logo=docker&style=flat
+  :target: https://hub.docker.com/r/nipreps/petprep/tags/
   :alt: Docker image available!
 
 .. image:: https://codeocean.com/codeocean-assets/badge/open-in-code-ocean.svg
@@ -37,37 +37,37 @@ task-based and resting-state functional MRI (fMRI).
 
 About
 -----
-.. image:: https://github.com/oesteban/fmriprep/raw/f4c7a9804be26c912b24ef4dccba54bdd72fa1fd/docs/_static/fmriprep-21.0.0.svg
+.. image:: https://github.com/oesteban/petprep/raw/f4c7a9804be26c912b24ef4dccba54bdd72fa1fd/docs/_static/petprep-21.0.0.svg
 
 
-*fMRIPrep* is a functional magnetic resonance imaging (fMRI) data
+*PETPrep* is a positron emission tomography (PET) data
 preprocessing pipeline that is designed to provide an easily accessible,
 state-of-the-art interface that is robust to variations in scan acquisition
 protocols and that requires minimal user input, while providing easily
 interpretable and comprehensive error and output reporting.
 It performs basic processing steps (coregistration, normalization, unwarping,
 noise component extraction, segmentation, skull-stripping, 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, and surface
+including PET imaging studies, graph theory measures, and surface
 or volume-based statistics.
 
 .. note::
 
-   *fMRIPrep* performs minimal preprocessing.
+   *PETPrep* performs minimal preprocessing.
    Here we define 'minimal preprocessing'  as motion correction, field
    unwarping, normalization, bias field correction, and brain extraction.
    See the `workflows section of our documentation
-   <https://fmriprep.readthedocs.io/en/latest/workflows.html>`__ for more details.
+   <https://petprep.readthedocs.io/en/latest/workflows.html>`__ for more details.
 
-The *fMRIPrep* pipeline uses a combination of tools from well-known software
+The *PETPrep* pipeline uses a combination of tools from well-known software
 packages, including FSL_, ANTs_, FreeSurfer_ and AFNI_.
 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 become available.
 
 This tool allows you to easily do the following:
 
-- Take fMRI data from raw to fully preprocessed form.
+- Take PET data from raw to fully preprocessed form.
 - Implement tools from different software packages.
 - Achieve optimal data processing quality by using the best tools available.
 - Generate preprocessing quality reports, with which the user can easily
@@ -78,11 +78,11 @@ This tool allows you to easily do the following:
   speed-up from manual processing or shell-scripted pipelines.
 
 More information and documentation can be found at
-https://fmriprep.readthedocs.io/
+https://petprep.readthedocs.io/
 
 Principles
 ----------
-*fMRIPrep* is built around three principles:
+*PETPrep* is built around three principles:
 
 1. **Robustness** - The pipeline adapts the preprocessing steps depending on
    the input dataset and should provide results as good as possible
@@ -93,7 +93,7 @@ Principles
    automatic fashion.
 3. **"Glass box"** philosophy - Automation should not mean that one should not
    visually inspect the results or understand the methods.
-   Thus, *fMRIPrep* provides visual reports for each subject, detailing the
+   Thus, *PETPrep* provides visual reports for each subject, detailing the
    accuracy of the most important processing steps.
    This, combined with the documentation, can help researchers to understand
    the process and decide which subjects should be kept for the group level
@@ -102,7 +102,7 @@ Principles
 Citation
 --------
 **Citation boilerplate**.
-Please acknowledge this work using the citation boilerplate that *fMRIPrep* includes
+Please acknowledge this work using the citation boilerplate that *PETPrep* includes
 in the visual report generated for every subject processed.
 For a more detailed description of the citation boilerplate and its relevance,
 please check out the
@@ -111,21 +111,21 @@ please check out the
 **Plagiarism disclaimer**.
 The boilerplate text is public domain, distributed under the
 `CC0 license <https://creativecommons.org/publicdomain/zero/1.0/>`__,
-and we recommend *fMRIPrep* users to reproduce it verbatim in their works.
+and we recommend *PETPrep* users to reproduce it verbatim in their works.
 Therefore, if reviewers and/or editors raise concerns because the text is flagged by automated
 plagiarism detection, please refer them to the *NiPreps* community and/or the note to this
 effect in the `boilerplate documentation page <https://www.nipreps.org/intro/transparency/#citation-boilerplates>`__.
 
 **Papers**.
-*fMRIPrep* contributors have published two relevant papers:
+*PETPrep* contributors have published two relevant papers:
 `Esteban et al. (2019) <https://doi.org/10.1038/s41592-018-0235-4>`__
 [`preprint <https://doi.org/10.1101/306951>`__], and
 `Esteban et al. (2020) <https://doi.org/10.1038/s41596-020-0327-3>`__
 [`preprint <https://doi.org/10.1101/694364>`__].
 
 **Other**.
 Other materials that have been generated over time include the
-`OHBM 2018 software demonstration <https://effigies.github.io/fmriprep-demo/>`__
+`OHBM 2018 software demonstration <https://effigies.github.io/petprep-demo/>`__
 and some conference posters:
 
 * Organization for Human Brain Mapping 2018
@@ -144,15 +144,15 @@ and some conference posters:
 
 License information
 -------------------
-*fMRIPrep* adheres to the
+*PETPrep* adheres to the
 `general licensing guidelines <https://www.nipreps.org/community/licensing/>`__
 of the *NiPreps framework*.
 
 License
 ~~~~~~~
 Copyright (c) the *NiPreps* Developers.
 
-As of the 21.0.x pre-release and release series, *fMRIPrep* is
+As of the 21.0.x pre-release and release series, *PETPrep* 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

docs/Makefile

@@ -9,7 +9,7 @@ BUILDDIR      = _build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-	$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from https://www.sphinx-doc.org/)
+	$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don''t have Sphinx installed, grab it from https://www.sphinx-doc.org/)
 endif
 
 # Internal variables.
@@ -96,9 +96,9 @@ qthelp:
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/fMRIprep.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PETPrep.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/fMRIprep.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PETPrep.qhc"
 
 .PHONY: applehelp
 applehelp:
@@ -115,8 +115,8 @@ devhelp:
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/fMRIprep"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/fMRIprep"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PETPrep"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PETPrep"
 	@echo "# devhelp"
 
 .PHONY: epub

docs/_static/sbatch.slurm

@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-#SBATCH -J fmriprep
+#SBATCH -J petprep
 #SBATCH --time=48:00:00
 #SBATCH -n 1
 #SBATCH --cpus-per-task=16
@@ -14,12 +14,12 @@
 # ------------------------------------------
 
 BIDS_DIR="$STUDY/data"
-DERIVS_DIR="derivatives/fmriprep-1.5.0"
+DERIVS_DIR="derivatives/petprep-1.5.0"
 LOCAL_FREESURFER_DIR="$STUDY/data/derivatives/freesurfer-6.0.1"
 
 # Prepare some writeable bind-mount points.
 TEMPLATEFLOW_HOST_HOME=$HOME/.cache/templateflow
-FMRIPREP_HOST_CACHE=$HOME/.cache/fmriprep
+FMRIPREP_HOST_CACHE=$HOME/.cache/petprep
 mkdir -p ${TEMPLATEFLOW_HOST_HOME}
 mkdir -p ${FMRIPREP_HOST_CACHE}
 
@@ -31,7 +31,7 @@ export SINGULARITYENV_FS_LICENSE=$HOME/.freesurfer.txt
 
 # Designate a templateflow bind-mount point
 export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow"
-SINGULARITY_CMD="singularity run --cleanenv -B $BIDS_DIR:/data -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} -B $L_SCRATCH:/work -B ${LOCAL_FREESURFER_DIR}:/fsdir $STUDY/images/nipreps_fmriprep_1.5.0.simg"
+SINGULARITY_CMD="singularity run --cleanenv -B $BIDS_DIR:/data -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} -B $L_SCRATCH:/work -B ${LOCAL_FREESURFER_DIR}:/fsdir $STUDY/images/nipreps_petprep_1.5.0.simg"
 
 # Parse the participants.tsv file and extract one subject ID from the line corresponding to this SLURM task.
 subject=$( sed -n -E "$((${SLURM_ARRAY_TASK_ID} + 1))s/sub-(\S*)\>.*/\1/gp" ${BIDS_DIR}/participants.tsv )

docs/api.rst

@@ -5,15 +5,15 @@ Developers - API
 ================
 The *NiPreps* community and contributing guidelines
 ---------------------------------------------------
-*fMRIPrep* is a *NiPreps* application, and abides by the
+*PETPrep* is a *NiPreps* application, and abides by the
 `NiPreps Community guidelines <https://www.nipreps.org/community/>`__.
 Please, make sure you have read and understood all the documentation
 provided in the `NiPreps portal <https://www.nipreps.org>`__ before
 you get started.
 
 Setting up your development environment
 ---------------------------------------
-We believe that *fMRIPrep* must be free to use, inspect, and critique.
+We believe that *PETPrep* must be free to use, inspect, and critique.
 Correspondingly, you should be free to modify our software to improve it
 or adapt it to new use cases and we especially welcome contributions to
 improve it or its documentation.
@@ -27,12 +27,12 @@ to help minimize your burden if you want to modify the software.
 Internal configuration system
 -----------------------------
 
-.. automodule:: fmriprep.config
+.. automodule:: petprep.config
    :members: from_dict, load, get, dumps, to_filename, init_spaces
 
 Workflows
 ---------
 
-.. automodule:: fmriprep.workflows.base
-.. automodule:: fmriprep.workflows.pet
-.. automodule:: fmriprep.workflows.pet.fit
+.. automodule:: petprep.workflows.base
+.. automodule:: petprep.workflows.pet
+.. automodule:: petprep.workflows.pet.fit

docs/benchmarks.rst

@@ -17,10 +17,10 @@ Datasets
 | B          | 2 T1w, 6 PEPolar fieldmaps, 8 SE-BOLD (4274 volumes total)                             |
 +------------+----------------------------------------------------------------------------------------+
 
-fMRIPrep versions and modes
+PETPrep versions and modes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-All commands took the form ``fmriprep sourcedata/raw . participant $OPTIONS``.
+All commands took the form ``petprep sourcedata/raw . participant $OPTIONS``.
 The specific options for each version or mode are presented in the following table.
 
 +------------+----------------------------------------------------------------------------------------+
@@ -46,7 +46,7 @@ Tests were run on a desktop machine running no other significant tests.
 * Memory: 64GiB
 * Storage: PC801 NVMe SK hynix 2TB
 * OS: Ubuntu 22.04
-* Environment: Docker images published to https://hub.docker.com/r/nipreps/fmriprep/
+* Environment: Docker images published to https://hub.docker.com/r/nipreps/petprep/
 
 Benchmarks
 ----------

docs/conf.py

@@ -1,4 +1,4 @@
-# fmriprep documentation build configuration file, created by
+# petprep documentation build configuration file, created by
 # sphinx-quickstart on Mon May  9 09:04:25 2016.
 #
 # This file is execfile()d with the current directory set to its
@@ -85,8 +85,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'fmriprep'
-author = 'The fMRIPrep developers'
+project = 'petprep'
+author = 'The PETPrep developers'
 copyright = f'2016-, {author}'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -160,7 +160,7 @@
 
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
-# html_title = u'fmriprep vversion'
+# html_title = u'petprep vversion'
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None
@@ -242,7 +242,7 @@
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'fmriprepdoc'
+htmlhelp_basename = 'petprepdoc'
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -261,7 +261,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'fmriprep.tex', 'fMRIprep Documentation', author, 'manual'),
+    (master_doc, 'petprep.tex', 'PETPrep Documentation', author, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -289,7 +289,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, 'fmriprep', 'fmriprep Documentation', [author], 1)]
+man_pages = [(master_doc, 'petprep', 'petprep Documentation', [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -303,10 +303,10 @@
 texinfo_documents = [
     (
         master_doc,
-        'fmriprep',
-        'fMRIprep Documentation',
+        'petprep',
+        'PETPrep Documentation',
         author,
-        'fmriprep',
+        'petprep',
         'One line description of project.',
         'Miscellaneous',
     ),
@@ -326,8 +326,8 @@
 
 # The following is used by sphinx.ext.linkcode to provide links to github
 linkcode_resolve = make_linkcode_resolve(
-    'fmriprep',
-    'https://github.com/nipreps/fmriprep/blob/{revision}/{package}/{path}#L{lineno}',
+    'petprep',
+    'https://github.com/nipreps/petprep/blob/{revision}/{package}/{path}#L{lineno}',
 )
 
 # Example configuration for intersphinx: refer to the Python standard library.