From 9d6ca9ffb72ea340abcf634039e95a70f5b71aa4 Mon Sep 17 00:00:00 2001 From: Hao-Ting Wang Date: Fri, 12 Apr 2024 15:21:40 -0400 Subject: [PATCH] JOSS submision (#118) * ADD basic info of the paper skip code spell on paper because it doesn't handle french * draft * fix joss workflow file name * FIX author syntax * FIX output path * FIX nilearn contributors * FIX typesetting * update RRID for projects that have them * Add Remi's details Co-authored-by: Remi Gau * Add Quentin's details (#123) * Add N. Clarke orcid (#124) * ADD PB affiliations * make sure the paper changes don't trigger unrelated workflows * Mark the date for submission * FIX don't trigger test workflow on irrelevant PR * point to the latest doc in joss link * Formatting --------- Co-authored-by: Remi Gau Co-authored-by: Quentin Dessain <5383293+Hyedryn@users.noreply.github.com> Co-authored-by: Natasha Clarke <57987005+clarkenj@users.noreply.github.com> --- .github/workflows/draft-paper.yml | 27 +++ .github/workflows/test.yml | 1 + .pre-commit-config.yaml | 1 + CITATION.cff | 9 +- paper/paper.bib | 281 ++++++++++++++++++++++++++++++ paper/paper.md | 133 ++++++++++++++ 6 files changed, 449 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/draft-paper.yml create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/.github/workflows/draft-paper.yml b/.github/workflows/draft-paper.yml new file mode 100644 index 0000000..d411e94 --- /dev/null +++ b/.github/workflows/draft-paper.yml @@ -0,0 +1,27 @@ +on: + pull_request: + push: + branches: [main] + paths: ['paper/*'] + +jobs: + paper: + runs-on: ubuntu-latest + name: Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Build draft PDF + uses: openjournals/openjournals-draft-action@master + with: + journal: joss + # This should be the path to the paper within your repo. + paper-path: paper/paper.md + - name: Upload + uses: actions/upload-artifact@v1 + with: + name: paper + # This is the output path where Pandoc will write the compiled + # PDF. Note, this should be the same directory as the input + # paper.md + path: paper/paper.pdf diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5da91c7..7afd375 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -10,6 +10,7 @@ on: branches: - main - maint/* + paths: ['giga_connectome/*', 'pyproject.toml', 'requirements.txt', 'Dockerfile'] defaults: run: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3157e2c..d070b36 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -27,6 +27,7 @@ repos: additional_dependencies: - tomli args: ["--skip=*.svg"] + exclude: 'paper/.*' - repo: https://github.com/PyCQA/flake8 rev: 7.0.0 hooks: diff --git a/CITATION.cff b/CITATION.cff index edf41fa..7d4330e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -20,10 +20,13 @@ authors: - family-names: Wang given-names: Hao-Ting email: htwangtw@gmail.com + - family-names: Gau + given-names: Rémi - family-names: Dessain given-names: Quentin - - family-names: Natasha - given-names: Clarke - + - family-names: Clarke + given-names: Natasha + - family-names: Bellec + given-names: Pierre license: MIT diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 0000000..a4d3061 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,281 @@ +@software{Nilearn, + author = {{Nilearn contributors}}, + license = {BSD-4-Clause}, + title = {{nilearn}}, + year = {2024}, + url = {https://github.com/nilearn/nilearn}, + doi = {10.5281/zenodo.8397156} +} + +@article{fmriprep, + title = {{fMRIPrep}: a robust preprocessing pipeline for functional {MRI}}, + volume = {16}, + issn = {1548-7091, 1548-7105}, + doi = {10.1038/s41592-018-0235-4}, + number = {1}, + journal = {Nature Methods}, + author = {Esteban, Oscar and Markiewicz, Christopher J. and Blair, Ross W. and Moodie, Craig A. and Isik, A. Ilkay and Erramuzpe, Asier and Kent, James D. and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit S. and Wright, Jessey and Durnez, Joke and Poldrack, Russell A. and Gorgolewski, Krzysztof J.}, + month = jan, + year = {2019}, + pages = {111--116}, +} + +@article{bidsapp, + title = {{BIDS} apps: {Improving} ease of use, accessibility, and reproducibility of neuroimaging data analysis methods}, + volume = {13}, + issn = {1553-7358}, + doi = {10.1371/journal.pcbi.1005209}, + number = {3}, + journal = {PLOS Computational Biology}, + author = {Gorgolewski, Krzysztof J. and Alfaro-Almagro, Fidel and Auer, Tibor and Bellec, Pierre and Capotă, Mihai and Chakravarty, M. Mallar and Churchill, Nathan W. and Cohen, Alexander Li and Craddock, R. Cameron and Devenyi, Gabriel A. and Eklund, Anders and Esteban, Oscar and Flandin, Guillaume and Ghosh, Satrajit S. and Guntupalli, J. Swaroop and Jenkinson, Mark and Keshavan, Anisha and Kiar, Gregory and Liem, Franziskus and Raamana, Pradeep Reddy and Raffelt, David and Steele, Christopher J. and Quirion, Pierre-Olivier and Smith, Robert E. and Strother, Stephen C. and Varoquaux, Gaël and Wang, Yida and Yarkoni, Tal and Poldrack, Russell A.}, + month = mar, + year = {2017}, + pages = {e1005209}, +} + +@article{bids, + title = {The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments}, + volume = {3}, + issn = {2052-4463}, + doi = {10.1038/sdata.2016.44}, + number = {1}, + journal = {Scientific Data}, + author = {Gorgolewski, Krzysztof J. and Auer, Tibor and Calhoun, Vince D. and Craddock, R. Cameron and Das, Samir and Duff, Eugene P. and Flandin, Guillaume and Ghosh, Satrajit S. and Glatard, Tristan and Halchenko, Yaroslav O. and Handwerker, Daniel A. and Hanke, Michael and Keator, David and Li, Xiangrui and Michael, Zachary and Maumet, Camille and Nichols, B. Nolan and Nichols, Thomas E. and Pellman, John and Poline, Jean-Baptiste and Rokem, Ariel and Schaefer, Gunnar and Sochat, Vanessa and Triplett, William and Turner, Jessica A. and Varoquaux, Gaël and Poldrack, Russell A.}, + month = jun, + year = {2016}, + pages = {160044}, +} + +@article{wang_continuous_2024, + title = {Continuous evaluation of denoising strategies in resting-state {fMRI} connectivity using {fMRIPrep} and {Nilearn}}, + volume = {20}, + issn = {1553-7358}, + doi = {10.1371/journal.pcbi.1011942}, + number = {3}, + urldate = {2024-03-28}, + journal = {PLOS Computational Biology}, + author = {Wang, Hao-Ting and Meisler, Steven L. and Sharmarke, Hanad and Clarke, Natasha and Gensollen, Nicolas and Markiewicz, Christopher J. and Paugam, François and Thirion, Bertrand and Bellec, Pierre}, + month = mar, + year = {2024}, + pages = {e1011942}, +} + +@article{templateflow, + title = {{TemplateFlow}: {FAIR}-sharing of multi-scale, multi-species brain models}, + volume = {19}, + issn = {1548-7105}, + shorttitle = {{TemplateFlow}}, + doi = {10.1038/s41592-022-01681-2}, + language = {en}, + number = {12}, + journal = {Nature Methods}, + author = {Ciric, Rastko and Thompson, William H. and Lorenz, Romy and Goncalves, Mathias and MacNicol, Eilidh E. and Markiewicz, Christopher J. and Halchenko, Yaroslav O. and Ghosh, Satrajit S. and Gorgolewski, Krzysztof J. and Poldrack, Russell A. and Esteban, Oscar}, + month = dec, + year = {2022}, + pages = {1568--1571}, +} + +@article{makris_decreased_2006, + title = {Decreased volume of left and total anterior insular lobule in schizophrenia}, + volume = {83}, + issn = {0920-9964}, + doi = {10.1016/j.schres.2005.11.020}, + number = {2-3}, + journal = {Schizophrenia Research}, + author = {Makris, Nikos and Goldstein, Jill M. and Kennedy, David and Hodge, Steven M. and Caviness, Verne S. and Faraone, Stephen V. and Tsuang, Ming T. and Seidman, Larry J.}, + month = apr, + year = {2006}, + pmid = {16448806}, + pages = {155--171}, +} + +@article{goldstein_hypothalamic_2007, + title = {Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability}, + volume = {61}, + issn = {0006-3223}, + shorttitle = {Hypothalamic abnormalities in schizophrenia}, + doi = {10.1016/j.biopsych.2006.06.027}, + language = {eng}, + number = {8}, + journal = {Biological Psychiatry}, + author = {Goldstein, Jill M. and Seidman, Larry J. and Makris, Nikos and Ahern, Todd and O'Brien, Liam M. and Caviness, Verne S. and Kennedy, David N. and Faraone, Stephen V. and Tsuang, Ming T.}, + month = apr, + year = {2007}, + pmid = {17046727}, + pages = {935--945}, +} + +@article{frazier_structural_2005, + title = {Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder}, + volume = {162}, + issn = {0002-953X}, + doi = {10.1176/appi.ajp.162.7.1256}, + language = {eng}, + number = {7}, + journal = {The American Journal of Psychiatry}, + author = {Frazier, Jean A. and Chiu, Sufen and Breeze, Janis L. and Makris, Nikos and Lange, Nicholas and Kennedy, David N. and Herbert, Martha R. and Bent, Eileen K. and Koneru, Vamsi K. and Dieterich, Megan E. and Hodge, Steven M. and Rauch, Scott L. and Grant, P. Ellen and Cohen, Bruce M. and Seidman, Larry J. and Caviness, Verne S. and Biederman, Joseph}, + month = jul, + year = {2005}, + pmid = {15994707}, + pages = {1256--1265}, +} + +@article{desikan_automated_2006, + title = {An automated labeling system for subdividing the human cerebral cortex on {MRI} scans into gyral based regions of interest}, + volume = {31}, + issn = {1053-8119}, + doi = {10.1016/j.neuroimage.2006.01.021}, + language = {eng}, + number = {3}, + journal = {NeuroImage}, + author = {Desikan, Rahul S. and Ségonne, Florent and Fischl, Bruce and Quinn, Brian T. and Dickerson, Bradford C. and Blacker, Deborah and Buckner, Randy L. and Dale, Anders M. and Maguire, R. Paul and Hyman, Bradley T. and Albert, Marilyn S. and Killiany, Ronald J.}, + month = jul, + year = {2006}, + pmid = {16530430}, + pages = {968--980}, +} + +@article{schaefer_local-global_2018, + title = {Local-{Global} {Parcellation} of the {Human} {Cerebral} {Cortex} from {Intrinsic} {Functional} {Connectivity} {MRI}}, + volume = {28}, + issn = {1460-2199}, + doi = {10.1093/cercor/bhx179}, + language = {eng}, + number = {9}, + journal = {Cerebral Cortex (New York, N.Y.: 1991)}, + author = {Schaefer, Alexander and Kong, Ru and Gordon, Evan M. and Laumann, Timothy O. and Zuo, Xi-Nian and Holmes, Avram J. and Eickhoff, Simon B. and Yeo, B. T. Thomas}, + month = sep, + year = {2018}, + pmid = {28981612}, + pmcid = {PMC6095216}, + pages = {3095--3114}, +} + +@article{urchs_mist_2019, + title = {{MIST}: {A} multi-resolution parcellation of functional brain networks}, + volume = {1}, + issn = {2515-5059}, + shorttitle = {{MIST}}, + doi = {10.12688/mniopenres.12767.2}, + language = {en}, + urldate = {2024-03-28}, + journal = {MNI Open Research}, + author = {Urchs, Sebastian and Armoza, Jonathan and Moreau, Clara and Benhajali, Yassine and St-Aubin, Jolène and Orban, Pierre and Bellec, Pierre}, + month = mar, + year = {2019}, + pages = {3}, +} + +@article{dadi_fine-grain_2020, + title = {Fine-grain atlases of functional modes for {fMRI} analysis}, + volume = {221}, + issn = {1053-8119}, + doi = {10.1016/j.neuroimage.2020.117126}, + urldate = {2024-03-28}, + journal = {NeuroImage}, + author = {Dadi, Kamalaker and Varoquaux, Gaël and Machlouzarides-Shalit, Antonia and Gorgolewski, Krzysztof J. and Wassermann, Demian and Thirion, Bertrand and Mensch, Arthur}, + month = nov, + year = {2020}, + pages = {117126}, +} + +@article{clarke_2024, + title = {Investigating the convergence of resting-state functional connectivity profiles in {Alzheimer}'s disease with neuropsychiatric symptoms and schizophrenia}, + author = {Clarke, Natasha and Moreau, Clara A. and Harvey, Annabelle and Wang, Hao-Ting and Orban, Pierre and Zahinoor, Ismail and Jacquemont, Sébastien and Bellec, Pierre}, + year = {2024}, + journal = {Brain Communications} +} + + +@article{HALFpipe, + title = {{ENIGMA} {HALFpipe}: {Interactive}, reproducible, and efficient analysis for resting-state and task-based {fMRI} data}, + volume = {43}, + issn = {1097-0193}, + doi = {10.1002/hbm.25829}, + language = {eng}, + number = {9}, + journal = {Human Brain Mapping}, + author = {Waller, Lea and Erk, Susanne and Pozzi, Elena and Toenders, Yara J. and Haswell, Courtney C. and Büttner, Marc and Thompson, Paul M. and Schmaal, Lianne and Morey, Rajendra A. and Walter, Henrik and Veer, Ilya M.}, + month = jun, + year = {2022}, + pmid = {35305030}, + pmcid = {PMC9120555}, + pages = {2727--2742}, +} + +@misc{cpac, + title = {Moving {Beyond} {Processing} and {Analysis}-{Related} {Variation} in {Neuroscience}}, + doi = {10.1101/2021.12.01.470790}, + language = {en}, + urldate = {2024-03-28}, + publisher = {bioRxiv}, + author = {Li, Xinhui and Esper, Nathalia Bianchini and Ai, Lei and Giavasis, Steve and Jin, Hecheng and Feczko, Eric and Xu, Ting and Clucas, Jon and Franco, Alexandre and Heinsfeld, Anibal Sólon and Adebimpe, Azeez and Vogelstein, Joshua T. and Yan, Chao-Gan and Esteban, Oscar and Poldrack, Russell A. and Craddock, Cameron and Fair, Damien and Satterthwaite, Theodore and Kiar, Gregory and Milham, Michael P.}, + month = jan, + year = {2024}, +} + +@article{conn, + title = {Conn: a functional connectivity toolbox for correlated and anticorrelated brain networks}, + volume = {2}, + issn = {2158-0022}, + doi = {10.1089/brain.2012.0073}, + language = {eng}, + number = {3}, + journal = {Brain Connectivity}, + author = {Whitfield-Gabrieli, Susan and Nieto-Castanon, Alfonso}, + year = {2012}, + pmid = {22642651}, + pages = {125--141}, +} + +@misc{xcp-d, + title = {{XCP}-{D}: {A} {Robust} {Pipeline} for the post-processing of {fMRI} data}, + shorttitle = {{XCP}-{D}}, + doi = {10.1101/2023.11.20.567926}, + language = {en}, + urldate = {2024-03-28}, + publisher = {bioRxiv}, + author = {Mehta, Kahini and Salo, Taylor and Madison, Thomas and Adebimpe, Azeez and Bassett, Danielle S. and Bertolero, Max and Cieslak, Matthew and Covitz, Sydney and Houghton, Audrey and Keller, Arielle S. and Luo, Audrey and Miranda-Dominguez, Oscar and Nelson, Steve M. and Shafiei, Golia and Shanmugan, Sheila and Shinohara, Russell T. and Sydnor, Valerie J. and Feczko, Eric and Fair, Damien A. and Satterthwaite, Theodore D.}, + month = nov, + year = {2023}, +} + +@article{ABIDE, + title = {The {Autism} {Brain} {Imaging} {Data} {Exchange}: {Towards} {Large}-{Scale} {Evaluation} of the {Intrinsic} {Brain} {Architecture} in {Autism}}, + volume = {19}, + issn = {1359-4184}, + doi = {10.1038/mp.2013.78}, + number = {6}, + journal = {Molecular psychiatry}, + author = {Di Martino, Adriana and Yan, Chao-Gan and Li, Qingyang and Denio, Erin and Castellanos, Francisco X. and Alaerts, Kaat and Anderson, Jeffrey S. and Assaf, Michal and Bookheimer, Susan Y. and Dapretto, Mirella and Deen, Ben and Delmonte, Sonja and Dinstein, Ilan and Ertl-Wagner, Birgit and Fair, Damien A. and Gallagher, Louise and Kennedy, Daniel P. and Keown, Christopher L. and Keysers, Christian and Lainhart, Janet E. and Lord, Catherine and Luna, Beatriz and Menon, Vinod and Minshew, Nancy and Monk, Christopher S. and Mueller, Sophia and Müller, Ralph-Axel and Nebel, Mary Beth and Nigg, Joel T. and O’Hearn, Kirsten and Pelphrey, Kevin A. and Peltier, Scott J. and Rudie, Jeffrey D. and Sunaert, Stefan and Thioux, Marc and Tyszka, J. Michael and Uddin, Lucina Q. and Verhoeven, Judith S. and Wenderoth, Nicole and Wiggins, Jillian L. and Mostofsky, Stewart H. and Milham, Michael P.}, + month = jun, + year = {2014}, + pmid = {23774715}, + pmcid = {PMC4162310}, + pages = {659--667}, +} + +@article{ukbiobank, + title = {{UK} {Biobank}: {An} {Open} {Access} {Resource} for {Identifying} the {Causes} of a {Wide} {Range} of {Complex} {Diseases} of {Middle} and {Old} {Age}}, + volume = {12}, + issn = {1549-1676}, + doi = {10.1371/journal.pmed.1001779}, + language = {en}, + number = {3}, + journal = {PLOS Medicine}, + author = {Sudlow, Cathie and Gallacher, John and Allen, Naomi and Beral, Valerie and Burton, Paul and Danesh, John and Downey, Paul and Elliott, Paul and Green, Jane and Landray, Martin and Liu, Bette and Matthews, Paul and Ong, Giok and Pell, Jill and Silman, Alan and Young, Alan and Sprosen, Tim and Peakman, Tim and Collins, Rory}, + month = mar, + year = {2015}, + pages = {e1001779}, +} + +@article{adhd200, + title = {The adhd-200 consortium: a model to advance the translational potential of neuroimaging in clinical neuroscience}, + volume = {6}, + issn = {1662-5137}, + doi = {10.3389/fnsys.2012.00062}, + journal = {Frontiers in Systems Neuroscience}, + author = {Milham, Michael P. Ph D. and Fair, Damien PA-C. and Mennes, Maarten Ph D. and Mostofsky, Stewart H. M. D.}, + month = sep, + year = {2012} +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 0000000..f57ce07 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,133 @@ +--- +title: 'Giga Connectome: a BIDS-app for time series and functional connectome extraction' +tags: + - BIDS + - Python + - fMRI + - functional connectivity +authors: + - name: Hao-Ting Wang + corresponding: true + orcid: 0000-0003-4078-2038 + affiliation: "1,2" # (Multiple affiliations must be quoted) + - name: Rémi Gau + orcid: 0000-0002-1535-9767 + affiliation: 3 + - name: Natasha Clarke + orcid: 0000-0003-2455-3614 + affiliation: 1 + - name: Quentin Dessain + orcid: 0000-0002-7314-0413 + affiliation: 4 + - name: Pierre Bellec + orcid: 0000-0002-9111-0699 + affiliation: "1,2,5" +affiliations: +- name: Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Université de Montréal, Montréal, QC, Canada + index: 1 +- name: Psychology Department, University of Montreal, Montreal, Canada + index: 2 +- name: Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada. + index: 3 +- name: Institute of Information and Communication Technologies, Electronics and Applied Mathematics (ICTEAM), UCLouvain, Louvain-la-Neuve, Belgium + index: 4 +- name: Mila, University of Montreal, Montreal, Canada + index: 5 +date: 12 April 2024 +bibliography: paper.bib +--- + +# Summary + +Researchers perform two steps before Functional magnetic resonance imaging (fMRI) data analysis: +standardised preprocessing and customised denoising. +`fMRIPrep` [@fmriprep; RRID:SCR_016216], +a popular software in the neuroimaging community, is a common choice for preprocessing. +`fMRIPrep` performs minimal preprocessing, leaving a few steps for the end user: smoothing, denoising, and standardisation. +The present software, `giga-connectome`, +is a Brain Imaging Data Structure [BIDS; @bids; RRID:SCR_016124] +compliant container image that aims to perform these steps as well as extract time series signals and generate connectomes for machine learning applications. +All these steps are implemented with functions from `nilearn` [@Nilearn; RRID:SCR_001362], +a python library for machine learning in neuroimaging. + +The tool performs smoothing, denoising, and standardisation on voxel level data. +Smoothing is implemented with a 5mm full width at half maximum kernel and the user can change the kernel size based on the voxel size of their fMRI data. +For the denoising step, we built the workflow closely aligned with the design choice of `fmriprep` +and worked with the `fmriprep` developers while implementing a key Application Programming Interface (API), +`load_confounds`, implemented in the software library `nilearn`. +The tool provides some preset strategies based on @wang_continuous_2024 and the current long-term support release `fMRIPrep`. +Users can implement their own strategy using configuration files to directly interact with the `load_confounds` API. +The details of the process can be found in the [user documentation](https://giga-connectome.readthedocs.io/en/latest/workflow.html). +Finally the data is standardised as z-scores. + +The atlas for time series extraction was retrieved through `templateflow` [@templateflow; RRID:SCR_021876], +a brain template and atlas naming system with a Python API. +The container image provides some default atlases +(Harvard-Oxford [@makris_decreased_2006; @goldstein_hypothalamic_2007; @frazier_structural_2005; @desikan_automated_2006], +Schaefer [@schaefer_local-global_2018], +MIST [@urchs_mist_2019], +and DiFuMo [@dadi_fine-grain_2020]) that are already available in the `templateflow` repository. +Customised atlases will have to be formatted in `templateflow` convention and supplied using a configuration file. +We aim to include more default atlases when they are included in the `templateflow` repository. + +The time series extraction is implemented with `nilearn` objects `NiftiLabelsMasker` and `NiftiMapsMasker`. +The generated time series are used to construct connectomes calculated as Pearson's correlation with `nilearn` object `ConnectivityMeasure`. + +Finally the saved time series and connectomes follow the format of +[BIDS-connectome specification](https://bids.neuroimaging.io/bep017). +Users can follow the specification to interpret and retrieve the relevant results. +The coverage of the atlas is also included as a html visual report, provided by `nilearn.masker` for users to examine the quality of the atlas coverage. +More information about the usage, workflow, and outputs can be found on the +[official documentation](https://giga-connectome.readthedocs.io/en/latest/). + + +# Statement of need + +`giga-connectome` is created for large scale deployment on multiple `fMRIPrep` preprocessed neuroimaging datasets. +We aimed to create a tool that is lightweight in terms of code base complexity, software dependencies, and command line interface (CLI). +The current software follows the BIDS-apps API [@bidsapp] and is the first of its kind that creates outputs in the BIDS-connectome. +Both users and developers would benefit from the detailed definition of BIDS-apps API and BIDS-connectome for shared usage documentation and development guidelines. +The key dependencies of the software are python clients of BIDS or BIDS adjacent projects (`pyBIDS` and `templateflow` python client) and `nilearn`, +which is an open source library of high quality and with a clear development cycle for future maintenance. +We used configuration files to structure the choice of denoising strategies and brain atlas to avoid crowding the CLI and ensure the choices of the user are traceable. + +We aim to provide a lightweight alternative to other existing post-fMRIPrep processing software such as XCP-D [@xcp-d] +and HALFPipe [@HALFpipe], +or preprocessing software with fMRIPrep support such as C-PAC [@cpac] +and CONN [@conn; RRID:SCR_009550]. +These tools provide more flexibility and options for denoising and more types of downstream feature extraction for a wider range of fMRI analysis. +`giga-connectome` was intentionally designed with a narrow scope for quick deployment and the ease for machine learning researchers to adopt. +We hope this modular implementation can eventually be included as part of these existing workflows so all `fMRIPrep` outputs can share a time series and connectome extraction tool that's minimal and streamlined. +Furthermore, this lean design choice aims to reduce the barrier to learning the code base and the ease of on-boarding new contributors. +We hope this choice will invite more users to contribute to the tool and benefit from the open source neuroimaging community. + +`giga-connectome` has already been deployed on multiple large neuroimaging datasets such as +ABIDE [@ABIDE], +ADHD200 [@adhd200], +UK Biobank [@ukbiobank], +and more. +The generated time series and connectomes have been included in a registered report [@clarke_2024], +and various work under preparation in the [SIMEXP lab](https://github.com/SIMEXP/) +and [CNeuromod project](https://www.cneuromod.ca/). +The data processing scripts using `giga-connectome` can be found +[here for UK Biobank](https://github.com/Hyedryn/ukbb-scripts/tree/dev) +and [this repository](https://github.com/SIMEXP/giga_preprocess2) for the other datasets. + +# Acknowledgement + +The project was supported by the following fundings: +Digital Alliance Canada Resource Allocation Competition (RAC 1827 and RAC 4455) to PB, +Institut de Valorisation des Données projets de recherche stratégiques +(IVADO PFR3) to PB, +and Canadian Consortium on Neurodegeneration in Aging +(CCNA; team 9 "discovering new biomarkers") to PB, +the Courtois Foundation to PB, +and Institut national de recherche en sciences et technologies du numérique +(INRIA; Programme Équipes Associées - NeuroMind Team DRI-012229) to PB. +HTW is supported by IVADO postdoc fellowship. +NC is supported by IVADO postdoc fellowship. +QD is a research fellow of the Fonds de la Recherche Scientifique - FNRS of Belgium. +RG is supported by funding from the Chan Zuckerberg Initiative. +PB was funded by Fonds de Recherche du Québec - Santé. + +# Reference