-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #26 from Inria-Empenn/hugoblox-import-publications
Hugo Blox Builder - Import latest publications
- Loading branch information
Showing
26 changed files
with
737 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| @article{caeyenberghs_enigmas_2024, | ||
| author = {Caeyenberghs, Karen and Imms, Phoebe and Irimia, Andrei and Monti, Martin M. and Esopenko, Carrie and De Souza, Nicola L. and Dominguez D, Juan F. and Newsome, Mary R. and Dobryakova, Ekaterina and Cwiek, Andrew and Mullin, Hollie A.C. and Kim, Nicholas J. and Mayer, Andrew R. and Adamson, Maheen M. and Bickart, Kevin and Breedlove, Katherine M. and Dennis, Emily L. and Disner, Seth G. and Haswell, Courtney and Hodges, Cooper B. and Hoskinson, Kristen R. and Johnson, Paula K. and Königs, Marsh and Li, Lucia M. and Liebel, Spencer W. and Livny, Abigail and Morey, Rajendra A. and Muir, Alexandra M. and Olsen, Alexander and Razi, Adeel and Su, Matthew and Tate, David F. and Velez, Carmen and Wilde, Elisabeth A. and Zielinski, Brandon A. and Thompson, Paul M. and Hillary, Frank G.}, | ||
| doi = {10.1016/j.nicl.2024.103585}, | ||
| file = {Caeyenberghs et al. - 2024 - ENIGMA’s simple seven Recommendations to enhance .pdf:/home/alpron/Zotero/storage/YQPWVWSN/Caeyenberghs et al. - 2024 - ENIGMA’s simple seven Recommendations to enhance .pdf:application/pdf}, | ||
| issn = {22131582}, | ||
| journal = {NeuroImage: Clinical}, | ||
| keywords = {Review, to read}, | ||
| language = {en}, | ||
| pages = {103585}, | ||
| shorttitle = {ENIGMA’s simple seven}, | ||
| title = {ENIGMA’s simple seven: Recommendations to enhance the reproducibility of resting-state fMRI in traumatic brain injury}, | ||
| url = {https://linkinghub.elsevier.com/retrieve/pii/S221315822400024X}, | ||
| urldate = {2024-08-12}, | ||
| volume = {42}, | ||
| year = {2024} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| --- | ||
| title: 'ENIGMA’s simple seven: Recommendations to enhance the reproducibility of resting-state | ||
| fMRI in traumatic brain injury' | ||
| authors: | ||
| - Karen Caeyenberghs | ||
| - Phoebe Imms | ||
| - Andrei Irimia | ||
| - Martin M. Monti | ||
| - Carrie Esopenko | ||
| - Nicola L. De Souza | ||
| - Juan F. Dominguez D | ||
| - Mary R. Newsome | ||
| - Ekaterina Dobryakova | ||
| - Andrew Cwiek | ||
| - Hollie A.C. Mullin | ||
| - Nicholas J. Kim | ||
| - Andrew R. Mayer | ||
| - Maheen M. Adamson | ||
| - Kevin Bickart | ||
| - Katherine M. Breedlove | ||
| - Emily L. Dennis | ||
| - Seth G. Disner | ||
| - Courtney Haswell | ||
| - Cooper B. Hodges | ||
| - Kristen R. Hoskinson | ||
| - Paula K. Johnson | ||
| - Marsh Königs | ||
| - Lucia M. Li | ||
| - Spencer W. Liebel | ||
| - Abigail Livny | ||
| - Rajendra A. Morey | ||
| - Alexandra M. Muir | ||
| - Alexander Olsen | ||
| - Adeel Razi | ||
| - Matthew Su | ||
| - David F. Tate | ||
| - Carmen Velez | ||
| - Elisabeth A. Wilde | ||
| - Brandon A. Zielinski | ||
| - Paul M. Thompson | ||
| - Frank G. Hillary | ||
| date: '2024-01-01' | ||
| publishDate: '2024-08-12T09:30:40.917271Z' | ||
| publication_types: | ||
| - article-journal | ||
| publication: '*NeuroImage: Clinical*' | ||
| doi: 10.1016/j.nicl.2024.103585 | ||
| tags: | ||
| - Review | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: https://linkinghub.elsevier.com/retrieve/pii/S221315822400024X | ||
| --- |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| @misc{cohen-adad_open_2024, | ||
| abstract = {This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducibility and the avoidance of pitfalls. It details practical applications from website management using GitHub Pages to organizing datasets in compliance with BIDS standards, highlights the importance of continuous testing for data integrity, IT management through Ansible for efficient system configuration, open source software development. The broader goal is to promote transparent, reproducible science by adopting open source tools. This approach not only saves time but exposes students to best practices, enhancing the transparency and reproducibility of scientific research.}, | ||
| author = {Cohen-Adad, Julien}, | ||
| file = {Cohen-Adad - 2024 - Open Source in Lab Management.html:/home/alpron/Zotero/storage/NSUKMR8S/Cohen-Adad - 2024 - Open Source in Lab Management.html:text/html;Cohen-Adad - 2024 - Open Source in Lab Management.pdf:/home/alpron/Zotero/storage/U8PYI68X/Cohen-Adad - 2024 - Open Source in Lab Management.pdf:application/pdf}, | ||
| keywords = {to read}, | ||
| month = {May}, | ||
| note = {arXiv:2405.07774 [cs]}, | ||
| publisher = {arXiv}, | ||
| title = {Open Source in Lab Management}, | ||
| url = {http://arxiv.org/abs/2405.07774}, | ||
| urldate = {2024-08-09}, | ||
| year = {2024} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| --- | ||
| title: Open Source in Lab Management | ||
| authors: | ||
| - Julien Cohen-Adad | ||
| date: '2024-05-01' | ||
| publishDate: '2024-08-12T09:30:40.850500Z' | ||
| publication_types: | ||
| - manuscript | ||
| publication: '*arXiv*' | ||
| abstract: This document explores the advantages of integrating open source software | ||
| and practices in managing a scientific lab, emphasizing reproducibility and the | ||
| avoidance of pitfalls. It details practical applications from website management | ||
| using GitHub Pages to organizing datasets in compliance with BIDS standards, highlights | ||
| the importance of continuous testing for data integrity, IT management through Ansible | ||
| for efficient system configuration, open source software development. The broader | ||
| goal is to promote transparent, reproducible science by adopting open source tools. | ||
| This approach not only saves time but exposes students to best practices, enhancing | ||
| the transparency and reproducibility of scientific research. | ||
| tags: | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: http://arxiv.org/abs/2405.07774 | ||
| --- |
19 changes: 19 additions & 0 deletions
19
content/publication/desrosiers-gregoire-standardized-2024/cite.bib
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| @article{desrosiers-gregoire_standardized_2024, | ||
| abstract = {Abstract | ||
| Functional magnetic resonance imaging in rodents holds great potential for advancing our understanding of brain networks. Unlike the human community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences, is a pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, this software platform will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.}, | ||
| author = {Desrosiers-Grégoire, Gabriel and Devenyi, Gabriel A. and Grandjean, Joanes and Chakravarty, M. Mallar}, | ||
| doi = {10.1038/s41467-024-50826-8}, | ||
| file = {Desrosiers-Grégoire et al. - 2024 - A standardized image processing and data quality p.pdf:/home/alpron/Zotero/storage/3J874RHT/Desrosiers-Grégoire et al. - 2024 - A standardized image processing and data quality p.pdf:application/pdf}, | ||
| issn = {2041-1723}, | ||
| journal = {Nature Communications}, | ||
| keywords = {to read}, | ||
| language = {en}, | ||
| month = {August}, | ||
| number = {1}, | ||
| pages = {6708}, | ||
| title = {A standardized image processing and data quality platform for rodent fMRI}, | ||
| url = {https://www.nature.com/articles/s41467-024-50826-8}, | ||
| urldate = {2024-08-12}, | ||
| volume = {15}, | ||
| year = {2024} | ||
| } |
32 changes: 32 additions & 0 deletions
32
content/publication/desrosiers-gregoire-standardized-2024/index.md
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| --- | ||
| title: A standardized image processing and data quality platform for rodent fMRI | ||
| authors: | ||
| - Gabriel Desrosiers-Grégoire | ||
| - Gabriel A. Devenyi | ||
| - Joanes Grandjean | ||
| - M. Mallar Chakravarty | ||
| date: '2024-08-01' | ||
| publishDate: '2024-08-12T09:30:40.857230Z' | ||
| publication_types: | ||
| - article-journal | ||
| publication: '*Nature Communications*' | ||
| doi: 10.1038/s41467-024-50826-8 | ||
| abstract: Abstract Functional magnetic resonance imaging in rodents holds great potential | ||
| for advancing our understanding of brain networks. Unlike the human community, there | ||
| remains no standardized resource in rodents for image processing, analysis and quality | ||
| control, posing significant reproducibility limitations. Our software platform, | ||
| Rodent Automated Bold Improvement of EPI Sequences, is a pipeline designed to address | ||
| these limitations for preprocessing, quality control, and confound correction, along | ||
| with best practices for reproducibility and transparency. We demonstrate the robustness | ||
| of the preprocessing workflow by validating performance across multiple acquisition | ||
| sites and both mouse and rat data. Building upon a thorough investigation into data | ||
| quality metrics across acquisition sites, we introduce guidelines for the quality | ||
| control of network analysis and offer recommendations for addressing issues. Taken | ||
| together, this software platform will allow the emerging community to adopt reproducible | ||
| practices and foster progress in translational neuroscience. | ||
| tags: | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: https://www.nature.com/articles/s41467-024-50826-8 | ||
| --- |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| @article{karakuzu_qmri-bids_2022, | ||
| abstract = {Abstract | ||
| The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store | ||
| multimodal | ||
| structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI through multicenter dissemination of interoperable datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. In conclusion, this BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the entrance barrier for qMRI in the field of neuroimaging.}, | ||
| author = {Karakuzu, Agah and Appelhoff, Stefan and Auer, Tibor and Boudreau, Mathieu and Feingold, Franklin and Khan, Ali R. and Lazari, Alberto and Markiewicz, Chris and Mulder, Martijn and Phillips, Christophe and Salo, Taylor and Stikov, Nikola and Whitaker, Kirstie and De Hollander, Gilles}, | ||
| doi = {10.1038/s41597-022-01571-4}, | ||
| file = {Karakuzu et al. - 2022 - qMRI-BIDS An extension to the brain imaging data .pdf:/home/alpron/Zotero/storage/J6M7GHA3/Karakuzu et al. - 2022 - qMRI-BIDS An extension to the brain imaging data .pdf:application/pdf}, | ||
| issn = {2052-4463}, | ||
| journal = {Scientific Data}, | ||
| keywords = {BIDS, to read}, | ||
| language = {en}, | ||
| month = {August}, | ||
| number = {1}, | ||
| pages = {517}, | ||
| shorttitle = {qMRI-BIDS}, | ||
| title = {qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data}, | ||
| url = {https://www.nature.com/articles/s41597-022-01571-4}, | ||
| urldate = {2024-08-12}, | ||
| volume = {9}, | ||
| year = {2022} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| --- | ||
| title: 'qMRI-BIDS: An extension to the brain imaging data structure for quantitative | ||
| magnetic resonance imaging data' | ||
| authors: | ||
| - Agah Karakuzu | ||
| - Stefan Appelhoff | ||
| - Tibor Auer | ||
| - Mathieu Boudreau | ||
| - Franklin Feingold | ||
| - Ali R. Khan | ||
| - Alberto Lazari | ||
| - Chris Markiewicz | ||
| - Martijn Mulder | ||
| - Christophe Phillips | ||
| - Taylor Salo | ||
| - Nikola Stikov | ||
| - Kirstie Whitaker | ||
| - Gilles De Hollander | ||
| date: '2022-08-01' | ||
| publishDate: '2024-08-12T09:30:40.864391Z' | ||
| publication_types: | ||
| - article-journal | ||
| publication: '*Scientific Data*' | ||
| doi: 10.1038/s41597-022-01571-4 | ||
| abstract: Abstract The Brain Imaging Data Structure (BIDS) established community | ||
| consensus on the organization of data and metadata for several neuroimaging modalities. | ||
| Traditionally, BIDS had a strong focus on functional magnetic resonance imaging | ||
| (MRI) datasets and lacked guidance on how to store multimodal structural MRI datasets. | ||
| Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds | ||
| a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim | ||
| of qMRI is to characterize brain microstructure by quantifying the physical MR parameters | ||
| of the tissue via computational, biophysical models. By proposing this new standard, | ||
| we envision standardization of qMRI through multicenter dissemination of interoperable | ||
| datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods | ||
| development and application-driven neuroimaging studies that can help develop quantitative | ||
| biomarkers for neural tissue characterization. In conclusion, this BIDS extension | ||
| offers a common ground for developers to exchange novel imaging data and tools, | ||
| reducing the entrance barrier for qMRI in the field of neuroimaging. | ||
| tags: | ||
| - BIDS | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: https://www.nature.com/articles/s41597-022-01571-4 | ||
| --- |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| @article{li_moving_2024, | ||
| author = {Li, Xinhui and Bianchini Esper, Nathalia and Ai, Lei and Giavasis, Steve and Jin, Hecheng and Feczko, Eric and Xu, Ting and Clucas, Jon and Franco, Alexandre and Sólon Heinsfeld, Anibal 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.}, | ||
| doi = {10.1038/s41562-024-01942-4}, | ||
| issn = {2397-3374}, | ||
| journal = {Nature Human Behaviour}, | ||
| keywords = {fMRI, to read}, | ||
| language = {en}, | ||
| month = {August}, | ||
| title = {Moving beyond processing- and analysis-related variation in resting-state functional brain imaging}, | ||
| url = {https://www.nature.com/articles/s41562-024-01942-4}, | ||
| urldate = {2024-08-12}, | ||
| year = {2024} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| --- | ||
| title: Moving beyond processing- and analysis-related variation in resting-state functional | ||
| brain imaging | ||
| authors: | ||
| - Xinhui Li | ||
| - Nathalia Bianchini Esper | ||
| - Lei Ai | ||
| - Steve Giavasis | ||
| - Hecheng Jin | ||
| - Eric Feczko | ||
| - Ting Xu | ||
| - Jon Clucas | ||
| - Alexandre Franco | ||
| - Anibal Sólon Heinsfeld | ||
| - Azeez Adebimpe | ||
| - Joshua T. Vogelstein | ||
| - Chao-Gan Yan | ||
| - Oscar Esteban | ||
| - Russell A. Poldrack | ||
| - Cameron Craddock | ||
| - Damien Fair | ||
| - Theodore Satterthwaite | ||
| - Gregory Kiar | ||
| - Michael P. Milham | ||
| date: '2024-08-01' | ||
| publishDate: '2024-08-12T09:30:40.902410Z' | ||
| publication_types: | ||
| - article-journal | ||
| publication: '*Nature Human Behaviour*' | ||
| doi: 10.1038/s41562-024-01942-4 | ||
| tags: | ||
| - fMRI | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: https://www.nature.com/articles/s41562-024-01942-4 | ||
| --- |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| @article{makowski_quality_2024, | ||
| author = {Makowski, Carolina and Nichols, Thomas E. and Dale, Anders M.}, | ||
| doi = {10.1038/s41386-024-01893-4}, | ||
| issn = {0893-133X, 1740-634X}, | ||
| journal = {Neuropsychopharmacology}, | ||
| keywords = {to read}, | ||
| language = {en}, | ||
| month = {June}, | ||
| shorttitle = {Quality over quantity}, | ||
| title = {Quality over quantity: powering neuroimaging samples in psychiatry}, | ||
| url = {https://www.nature.com/articles/s41386-024-01893-4}, | ||
| urldate = {2024-08-12}, | ||
| year = {2024} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| --- | ||
| title: 'Quality over quantity: powering neuroimaging samples in psychiatry' | ||
| authors: | ||
| - Carolina Makowski | ||
| - Thomas E. Nichols | ||
| - Anders M. Dale | ||
| date: '2024-06-01' | ||
| publishDate: '2024-08-12T09:30:40.924928Z' | ||
| publication_types: | ||
| - article-journal | ||
| publication: '*Neuropsychopharmacology*' | ||
| doi: 10.1038/s41386-024-01893-4 | ||
| tags: | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: https://www.nature.com/articles/s41386-024-01893-4 | ||
| --- |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| @article{mehta_xcp-d_2024, | ||
| abstract = {Abstract | ||
| Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they may not support output from different pre-processing pipelines, may have limited documentation, and may not follow generally accepted data organization standards (e.g. BIDS). In response, we present XCP-D: a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University of Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Apptainer image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NIfTI or CIFTI files following pre-processing with fMRIPrep, HCP, or ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >5,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.}, | ||
| author = {Mehta, Kahini and Salo, Taylor and Madison, Thomas J. and Adebimpe, Azeez and Bassett, Danielle S. and Bertolero, Max and Cieslak, Matthew and Covitz, Sydney and Houghton, Audrey and Keller, Arielle S. and Lundquist, Jacob T. and Luo, Audrey and Miranda-Dominguez, Oscar and Nelson, Steve M. and Shafiei, Golia and Shanmugan, Sheila and Shinohara, Russell T. and Smyser, Christopher D. and Sydnor, Valerie J. and Weldon, Kimberly B. and Feczko, Eric and Fair, Damien A. and Satterthwaite, Theodore D.}, | ||
| doi = {10.1162/imag_a_00257}, | ||
| issn = {2837-6056}, | ||
| journal = {Imaging Neuroscience}, | ||
| keywords = {fMRI, to read}, | ||
| language = {en}, | ||
| month = {July}, | ||
| shorttitle = {XCP-D}, | ||
| title = {XCP-D: A Robust Pipeline for the Post-Processing of fMRI data}, | ||
| url = {https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00257/123715/XCP-D-A-Robust-Pipeline-for-the-Post-Processing-of}, | ||
| urldate = {2024-08-12}, | ||
| year = {2024} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| --- | ||
| title: 'XCP-D: A Robust Pipeline for the Post-Processing of fMRI data' | ||
| authors: | ||
| - Kahini Mehta | ||
| - Taylor Salo | ||
| - Thomas J. Madison | ||
| - Azeez Adebimpe | ||
| - Danielle S. Bassett | ||
| - Max Bertolero | ||
| - Matthew Cieslak | ||
| - Sydney Covitz | ||
| - Audrey Houghton | ||
| - Arielle S. Keller | ||
| - Jacob T. Lundquist | ||
| - Audrey Luo | ||
| - Oscar Miranda-Dominguez | ||
| - Steve M. Nelson | ||
| - Golia Shafiei | ||
| - Sheila Shanmugan | ||
| - Russell T. Shinohara | ||
| - Christopher D. Smyser | ||
| - Valerie J. Sydnor | ||
| - Kimberly B. Weldon | ||
| - Eric Feczko | ||
| - Damien A. Fair | ||
| - Theodore D. Satterthwaite | ||
| date: '2024-07-01' | ||
| publishDate: '2024-08-12T09:30:40.909389Z' | ||
| publication_types: | ||
| - article-journal | ||
| publication: '*Imaging Neuroscience*' | ||
| doi: 10.1162/imag_a_00257 | ||
| abstract: 'Abstract Functional neuroimaging is an essential tool for neuroscience | ||
| research. Pre-processing pipelines produce standardized, minimally pre-processed | ||
| data to support a range of potential analyses. However, post-processing is not similarly | ||
| standardized. While several options for post-processing exist, they may not support | ||
| output from different pre-processing pipelines, may have limited documentation, | ||
| and may not follow generally accepted data organization standards (e.g. BIDS). In | ||
| response, we present XCP-D: a collaborative effort between PennLINC at the University | ||
| of Pennsylvania and the DCAN lab at the University of Minnesota. XCP-D uses an open | ||
| development model on GitHub and incorporates continuous integration testing; it | ||
| is distributed as a Docker container or Apptainer image. XCP-D generates denoised | ||
| BOLD images and functional derivatives from resting-state data in either NIfTI or | ||
| CIFTI files following pre-processing with fMRIPrep, HCP, or ABCD-BIDS pipelines. | ||
| Even prior to its official release, XCP-D has been downloaded >5,000 times from | ||
| DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing | ||
| of fMRI data.' | ||
| tags: | ||
| - fMRI | ||
| - to read | ||
| links: | ||
| - name: URL | ||
| url: | ||
| https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00257/123715/XCP-D-A-Robust-Pipeline-for-the-Post-Processing-of | ||
| --- |
Oops, something went wrong.