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Prepare for 1.0.0rc1 release #178

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90 changes: 0 additions & 90 deletions .zenodo.json

This file was deleted.

171 changes: 171 additions & 0 deletions CITATION.cff
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@@ -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: [email protected]
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'
10 changes: 5 additions & 5 deletions docs/building_workflows.rst
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Expand Up @@ -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.

Expand Down Expand Up @@ -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
Expand All @@ -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`.
Expand All @@ -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:
Expand Down
16 changes: 8 additions & 8 deletions docs/builtin_workflows.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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.
Expand All @@ -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``.

Expand All @@ -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`
Expand All @@ -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
Expand Down Expand Up @@ -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.

Expand Down
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