Prepare for 1.0.0rc1 release (#178)

* Create CITATION.cff

* Use consistent name.

* Add info on running tests locally.

* Add release notes for 1.0.0rc1.

* Remove unnecessary Zenodo file.

CITATION.cff

@@ -0,0 +1,171 @@
+cff-version: 1.2.0
+title: "QSIRecon: Reconstruction of preprocessed q-space images (dMRI)"
+message: If you use this software, please cite it using the following metadata.
+type: software
+authors:
+  - family-names: Cieslak
+    given-names: Matthew
+    affiliation: Department of Neuropsychiatry, University of Pennsylvania
+    orcid: https://orcid.org/0000-0002-1931-4734
+  - family-names: Camacho
+    given-names: Paul B.
+    affiliation: Beckman Institute for Advanced Science & Technology, University of Illinois at Urbana-Champaign, IL, USA
+    orcid: https://orcid.org/0000-0001-9048-7307
+  - family-names: Covitz
+    given-names: Sydney
+    affiliation: Perelman School of Medicine, University of Pennsylvania, PA, USA
+    orcid: https://orcid.org/0000-0002-7430-4125
+  - family-names: Foran
+    given-names: William
+    affiliation: Department of Psychiatry, University of Pittsburgh Medical Center
+    orcid: https://orcid.org/0000-0001-7491-9798
+  - family-names: He
+    given-names: Xiaosong
+    affiliation: Department of Bioengineering, University of Pennsylvania
+    orcid: https://orcid.org/0000-0002-7941-2918
+  - family-names: Humphries
+    given-names: Joseph
+    affiliation: Turing Medical
+    orcid: https://orcid.org/0000-0002-1025-7956
+  - family-names: Legarreta Gorroño
+    given-names: Jon Haitz
+    affiliation: Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School
+    orcid: https://orcid.org/0000-0002-9661-1396
+  - family-names: Magnussen
+    given-names: Fredrik
+    affiliation: Department of Psychology, University of Oslo
+    orcid: https://orcid.org/0000-0003-2574-1705
+  - family-names: Meisler
+    given-names: Steven Lee
+    affiliation: Harvard-MIT Program in Speech and Hearing Bioscience and Technology
+    orcid: https://orcid.org/0000-0002-8888-1572
+  - family-names: Krause
+    given-names: Michael
+    affiliation: Max Planck Institute for Human Development, Berlin, Germany
+    orcid: https://orcid.org/0000-0002-3878-6542
+  - family-names: Sadil
+    given-names: Patrick
+    affiliation: Johns Hopkins Bloomberg School of Public Health
+    orcid: https://orcid.org/0000-0003-4141-1343
+  - family-names: Salo
+    given-names: Taylor
+    email: salot@pennmedicine.upenn.edu
+    affiliation: University of Pennsylvania
+    orcid: https://orcid.org/0000-0001-9813-3167
+  - family-names: Sydnor
+    given-names: Valerie Jill
+    affiliation: Perelman School of Medicine, University of Pennsylvania
+    orcid: https://orcid.org/0000-0002-8640-668X
+  - family-names: Satterthwaite
+    given-names: Theodore D.
+    affiliation: Perelman School of Medicine, University of Pennsylvania, PA, USA
+    orcid: https://orcid.org/0000-0001-7072-9399
+preferred-citation:
+  type: article
+  authors:
+    - family-names: Cieslak
+      given-names: Matthew
+    - family-names: Cook
+      given-names: Philip A.
+    - family-names: He
+      given-names: Xiaosong
+    - family-names: Yeh
+      given-names: Fang-Cheng
+    - family-names: Dhollander
+      given-names: Thijs
+    - family-names: Adebimpe
+      given-names: Azeez
+    - family-names: Aguirre
+      given-names: Geoffrey K.
+    - family-names: Bassett
+      given-names: Danielle S.
+    - family-names: Betzel
+      given-names: Richard F.
+    - family-names: Bourque
+      given-names: Josiane
+    - family-names: Cabral
+      given-names: Laura M.
+    - family-names: Davatzikos
+      given-names: Christos
+    - family-names: Detre
+      given-names: John A.
+    - family-names: Earl
+      given-names: Eric
+    - family-names: Elliott
+      given-names: Mark A.
+    - family-names: Fadnavis
+      given-names: Shreyas
+    - family-names: Fair
+      given-names: Damien A.
+    - family-names: Foran
+      given-names: Will
+    - family-names: Fotiadis
+      given-names: Panagiotis
+    - family-names: Garyfallidis
+      given-names: Eleftherios
+    - family-names: Giesbrecht
+      given-names: Barry
+    - family-names: Gur
+      given-names: Ruben C.
+    - family-names: Gur
+      given-names: Raquel E.
+    - family-names: Kelz
+      given-names: Max B.
+    - family-names: Keshavan
+      given-names: Anisha
+    - family-names: Larsen
+      given-names: Bart S.
+    - family-names: Luna
+      given-names: Beatriz
+    - family-names: Mackey
+      given-names: Allyson P.
+    - family-names: Milham
+      given-names: Michael P.
+    - family-names: Oathes
+      given-names: Desmond J.
+    - family-names: Perrone
+      given-names: Anders
+    - family-names: Pines
+      given-names: Adam R.
+    - family-names: Roalf
+      given-names: David R.
+    - family-names: Richie-Halford
+      given-names: Adam
+    - family-names: Rokem
+      given-names: Ariel
+    - family-names: Sydnor
+      given-names: Valerie J.
+    - family-names: Tapera
+      given-names: Tinashe M.
+    - family-names: Tooley
+      given-names: Ursula A.
+    - family-names: Vettel
+      given-names: Jean M.
+    - family-names: Yeatman
+      given-names: Jason D.
+    - family-names: Grafton
+      given-names: Scott T.
+    - family-names: Satterthwaite
+      given-names: Theodore D.
+  doi: 10.1038/s41592-021-01185-5
+  journal: Nature Methods
+  start: 775
+  end: 778
+  title: 'QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data'
+  issue: 7
+  volume: 18
+  year: 2021
+repository-code: 'https://github.com/PennLINC/qsirecon'
+url: 'https://qsirecon.readthedocs.io'
+keywords:
+  - neuroimaging
+  - workflow
+  - pipeline
+  - postprocessing
+  - reconstruction
+  - dMRI
+  - BIDS
+  - BIDS-App
+license: BSD-3-Clause
+version: 1.0.0rc1
+date-released: '2024-11-20'

docs/building_workflows.rst

@@ -6,8 +6,8 @@
 Custom Reconstruction Workflows
 ###############################
 
-QSIRecon workflows are defined in ``YAML`` files. The :ref:`builtin_workflows`
-can be found in the QSIRecon ``YAML`` format on
+*QSIRecon* workflows are defined in ``YAML`` files. The :ref:`builtin_workflows`
+can be found in the *QSIRecon* ``YAML`` format on
 `github <https://github.com/PennLINC/qsirecon/tree/main/qsirecon/data/pipelines>`_,
 and are a great place to get started with customizing parts of these workflows.
 
@@ -37,7 +37,7 @@ based on the T1w or T2w images in the input data. Currently accepted values are
 Pipeline nodes
 **************
 
-A *node* in the QSIRecon ``"nodes"`` list represents a unit of processing.
+A *node* in the *QSIRecon* ``"nodes"`` list represents a unit of processing.
 Unlike NiPype nodes, which represent a single call to a commandline program
 or function, a node here represents a set of steps that accomplish a task.
 For example, if you want to perform CSD there are other steps that should
@@ -62,7 +62,7 @@ The entry for this in the ``"nodes"`` list could look like:
       qsirecon_suffix: MRtrix3_act-FAST
       software: MRTrix3
 
-QSIRecon figures out which software to use based on the values specified
+*QSIRecon* figures out which software to use based on the values specified
 for ``"software"`` and ``"action"``. The full list of recognized actions
 for each software package can be found in
 :meth:`qsirecon.workflows.build_workflow.workflow_from_spec`.
@@ -75,7 +75,7 @@ as an id for this node and is used for :ref:`passing_downstream`.
 Connecting Nodes
 ================
 
-Mixing between software packages is something QSIRecon generally does well.
+Mixing between software packages is something *QSIRecon* generally does well.
 There are a number of ways that nodes can exchange data with one another.
 
 .. _passing_downstream:

docs/builtin_workflows.rst

@@ -250,7 +250,7 @@ generated streamlines belong to the target tract based on the Hausdorff distance
 subject and atlas streamlines.
 
 Reconstructed subject-specific tracts are written out as .tck files that are aligned to the
-qsirecon-generated _dwiref.nii.gz and preproc_T1w.nii.gz volumes; .tck files can be visualized
+*QSIRecon*-generated _dwiref.nii.gz and preproc_T1w.nii.gz volumes; .tck files can be visualized
 overlaid on these volumes in mrview or MI-brain. Note, .tck files will not appear in alignment
 with the dwiref/T1w volumes in DSI Studio due to how the .tck files are read in.
 
@@ -389,8 +389,8 @@ Scalar Maps
 ``reorient_fslstd``
 ===================
 
-Reorients the ``qsirecon`` preprocessed DWI and bval/bvec to the standard FSL orientation.
-This can be useful if FSL tools will be applied outside of ``qsirecon``.
+Reorients the *QSIRecon* preprocessed DWI and bval/bvec to the standard FSL orientation.
+This can be useful if FSL tools will be applied outside of *QSIRecon*.
 
 
 .. _csdsi_3dshore:
@@ -517,7 +517,7 @@ Connectivity matrices
 *********************
 
 Instead of offering a bewildering number of options for constructing connectivity matrices,
-``qsirecon`` will construct as many connectivity matrices as it can given the reconstruction
+*QSIRecon* will construct as many connectivity matrices as it can given the reconstruction
 methods.
 It is **highly** recommended that you pick a weighting scheme before you run
 these pipelines and only look at those numbers.
@@ -532,7 +532,7 @@ To skip this step in your workflow, you can modify an existing recon pipeline by
 Atlases
 =======
 
-The following atlases are included in ``qsirecon``.
+The following atlases are included in *QSIRecon*.
 This means you do not need to add a ``--datasets`` argument to your command line,
 and can instead select them just with ``--atlases``.
 
@@ -548,7 +548,7 @@ If you use one of them please be sure to cite the relevant publication.
  * ``Gordon333Ext``: :footcite:t:`gordon2016generation`, extended with subcortical parcels.
  * ``AAL116``: :footcite:t:`tzourio2002automated`
 
-The ``qsirecon`` atlas set can be downloaded directly from
+The *QSIRecon* atlas set can be downloaded directly from
 `box  <https://upenn.box.com/shared/static/8k17yt2rfeqm3emzol5sa0j9fh3dhs0i.xz>`_.
 
 The 4S atlas combines the Schaefer 2018 cortical atlas (version v0143) :footcite:p:`Schaefer_2017`
@@ -559,7 +559,7 @@ the HCP thalamic atlas :footcite:p:`najdenovska2018vivo`,
 and the amygdala and hippocampus parcels from the HCP CIFTI subcortical parcellation
 :footcite:p:`glasser2013minimal`.
 The 4S atlas is used in the same manner across three PennLINC BIDS Apps:
-QSIRecon, XCP-D, and ASLPrep, to produce synchronized outputs across modalities.
+*QSIRecon*, *XCP-D*, and *ASLPrep*, to produce synchronized outputs across modalities.
 For more information about the 4S atlas, please see https://github.com/PennLINC/AtlasPack.
 
 Atlases are written out to the ``atlases`` subfolder, following
@@ -601,7 +601,7 @@ Users can control which atlases are used with the ``--atlases`` and ``--datasets
 
 The nifti images should be registered to the
 `MNI152NLin2009cAsym <https://github.com/PennLINC/qsirecon/blob/main/qsirecon/data/mni_1mm_t1w_lps.nii.gz>`_
-included in ``qsirecon``.
+included in *QSIRecon*.
 It is essential that your images are in the LPS+ orientation and have the sform zeroed-out in the header.
 **Be sure to check for alignment and orientation** in your outputs.