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126 results on '"Raamana, Pradeep Reddy"'

1. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Author

Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L, Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, galassi, anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G, Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W, Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, and Gorgolewski, Krzysztof J.

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

Published
2023
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3. Kernel methods library for pattern analysis and machine learning in python

Author

Raamana, Pradeep Reddy

Subjects
Computer Science - Machine Learning, Computer Science - Computer Vision and Pattern Recognition, Statistics - Computation, Statistics - Machine Learning
Abstract

Kernel methods have proven to be powerful techniques for pattern analysis and machine learning (ML) in a variety of domains. However, many of their original or advanced implementations remain in Matlab. With the incredible rise and adoption of Python in the ML and data science world, there is a clear need for a well-defined library that enables not only the use of popular kernels, but also allows easy definition of customized kernels to fine-tune them for diverse applications. The kernelmethods library fills that important void in the python ML ecosystem in a domain-agnostic fashion, allowing the sample data type to be anything from numerical, categorical, graphs or a combination of them. In addition, this library provides a number of well-defined classes to make various kernel-based operations efficient (for large scale datasets), modular (for ease of domain adaptation), and inter-operable (across different ecosystems). The library is available at https://github.com/raamana/kernelmethods., Comment: 6 pages, 3 code examples, 1 table

Published
2020

4. Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective

Author

Levitis, Elizabeth, van Praag, Cassandra D Gould, Gau, Rémi, Heunis, Stephan, DuPre, Elizabeth, Kiar, Gregory, Bottenhorn, Katherine L, Glatard, Tristan, Nikolaidis, Aki, Whitaker, Kirstie Jane, Mancini, Matteo, Niso, Guiomar, Afyouni, Soroosh, Alonso-Ortiz, Eva, Appelhoff, Stefan, Arnatkeviciute, Aurina, Atay, Selim Melvin, Auer, Tibor, Baracchini, Giulia, Bayer, Johanna MM, Beauvais, Michael JS, Bijsterbosch, Janine D, Bilgin, Isil P, Bollmann, Saskia, Bollmann, Steffen, Botvinik-Nezer, Rotem, Bright, Molly G, Calhoun, Vince D, Chen, Xiao, Chopra, Sidhant, Chuan-Peng, Hu, Close, Thomas G, Cookson, Savannah L, Craddock, R Cameron, De La Vega, Alejandro, De Leener, Benjamin, Demeter, Damion V, Di Maio, Paola, Dickie, Erin W, Eickhoff, Simon B, Esteban, Oscar, Finc, Karolina, Frigo, Matteo, Ganesan, Saampras, Ganz, Melanie, Garner, Kelly G, Garza-Villarreal, Eduardo A, Gonzalez-Escamilla, Gabriel, Goswami, Rohit, Griffiths, John D, Grootswagers, Tijl, Guay, Samuel, Guest, Olivia, Handwerker, Daniel A, Herholz, Peer, Heuer, Katja, Huijser, Dorien C, Iacovella, Vittorio, Joseph, Michael JE, Karakuzu, Agah, Keator, David B, Kobeleva, Xenia, Kumar, Manoj, Laird, Angela R, Larson-Prior, Linda J, Lautarescu, Alexandra, Lazari, Alberto, Legarreta, Jon Haitz, Li, Xue-Ying, Lv, Jinglei, L., Sina Mansour, Meunier, David, Moraczewski, Dustin, Nandi, Tulika, Nastase, Samuel A, Nau, Matthias, Noble, Stephanie, Norgaard, Martin, Obungoloch, Johnes, Oostenveld, Robert, Orchard, Edwina R, Pinho, Ana Luísa, Poldrack, Russell A, Qiu, Anqi, Raamana, Pradeep Reddy, Rokem, Ariel, Rutherford, Saige, Sharan, Malvika, Shaw, Thomas B, Syeda, Warda T, Testerman, Meghan M, Toro, Roberto, Valk, Sofie L, Van Den Bossche, Sofie, Varoquaux, Gaël, Váša, František, Veldsman, Michele, Vohryzek, Jakub, Wagner, Adina S, and Walsh, Reubs J

Subjects
online conferences, diversity, inclusivity, open science, collaborative events
Abstract

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

Published
2021

5. Assessing and tuning brain decoders: cross-validation, caveats, and guidelines

Author

Varoquaux, Gaël, Raamana, Pradeep Reddy, Engemann, Denis, Hoyos-Idrobo, Andrés, Schwartz, Yannick, and Thirion, Bertrand

Subjects
Statistics - Machine Learning
Abstract

Decoding, ie prediction from brain images or signals, calls for empirical evaluation of its predictive power. Such evaluation is achieved via cross-validation, a method also used to tune decoders' hyper-parameters. This paper is a review on cross-validation procedures for decoding in neuroimaging. It includes a didactic overview of the relevant theoretical considerations. Practical aspects are highlighted with an extensive empirical study of the common decoders in within-and across-subject predictions, on multiple datasets --anatomical and functional MRI and MEG-- and simulations. Theory and experiments outline that the popular " leave-one-out " strategy leads to unstable and biased estimates, and a repeated random splits method should be preferred. Experiments outline the large error bars of cross-validation in neuroimaging settings: typical confidence intervals of 10%. Nested cross-validation can tune decoders' parameters while avoiding circularity bias. However we find that it can be more favorable to use sane defaults, in particular for non-sparse decoders., Comment: NeuroImage, Elsevier, 2016

Published
2016
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7. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Author

Poldrack, R, Markiewicz, C, Appelhoff, S, Ashar, Y, Auer, T, Baillet, S, Bansal, S, Beltrachini, L, Benar, C, Bertazzoli, G, Bhogawar, S, Blair, R, Bortoletto, M, Boudreau, M, Brooks, T, Calhoun, V, Castelli, F, Clement, P, Cohen, A, Cohen-Adad, J, D'Ambrosio, S, de Hollander, G, de la Iglesia-Vayá, M, de la Vega, A, Delorme, A, Devinsky, O, Draschkow, D, Duff, E, Dupre, E, Earl, E, Esteban, O, Feingold, F, Flandin, G, Galassi, A, Gallitto, G, Ganz, M, Gau, R, Gholam, J, Ghosh, S, Giacomel, A, Gillman, A, Gleeson, P, Gramfort, A, Guay, S, Guidali, G, Halchenko, Y, Handwerker, D, Hardcastle, N, Herholz, P, Hermes, D, Honey, C, Innis, R, Ioanas, H, Jahn, A, Karakuzu, A, Keator, D, Kiar, G, Kincses, B, Laird, A, Lau, J, Lazari, A, Legarreta, J, Li, A, Li, X, Love, B, Lu, H, Marcantoni, E, Maumet, C, Mazzamuto, G, Meisler, S, Mikkelsen, M, Mutsaerts, H, Nichols, T, Nikolaidis, A, Nilsonne, G, Niso, G, Norgaard, M, Okell, T, Oostenveld, R, Ort, E, Park, P, Pawlik, M, Pernet, C, Pestilli, F, Petr, J, Phillips, C, Poline, J, Pollonini, L, Raamana, P, Ritter, P, Rizzo, G, Robbins, K, Rockhill, A, Rogers, C, Rokem, A, Rorden, C, Routier, A, Saborit-Torres, J, Salo, T, Schirner, M, Smith, R, Spisak, T, Sprenger, J, Swann, N, Szinte, M, Takerkart, S, Thirion, B, Thomas, A, Torabian, S, Varoquaux, G, Voytek, B, Welzel, J, Wilson, M, Yarkoni, T, Gorgolewski, K, Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L., Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la Iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, Galassi, Anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G., Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Marcantoni, Eleonora, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W., Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, Gorgolewski, Krzysztof J., Poldrack, R, Markiewicz, C, Appelhoff, S, Ashar, Y, Auer, T, Baillet, S, Bansal, S, Beltrachini, L, Benar, C, Bertazzoli, G, Bhogawar, S, Blair, R, Bortoletto, M, Boudreau, M, Brooks, T, Calhoun, V, Castelli, F, Clement, P, Cohen, A, Cohen-Adad, J, D'Ambrosio, S, de Hollander, G, de la Iglesia-Vayá, M, de la Vega, A, Delorme, A, Devinsky, O, Draschkow, D, Duff, E, Dupre, E, Earl, E, Esteban, O, Feingold, F, Flandin, G, Galassi, A, Gallitto, G, Ganz, M, Gau, R, Gholam, J, Ghosh, S, Giacomel, A, Gillman, A, Gleeson, P, Gramfort, A, Guay, S, Guidali, G, Halchenko, Y, Handwerker, D, Hardcastle, N, Herholz, P, Hermes, D, Honey, C, Innis, R, Ioanas, H, Jahn, A, Karakuzu, A, Keator, D, Kiar, G, Kincses, B, Laird, A, Lau, J, Lazari, A, Legarreta, J, Li, A, Li, X, Love, B, Lu, H, Marcantoni, E, Maumet, C, Mazzamuto, G, Meisler, S, Mikkelsen, M, Mutsaerts, H, Nichols, T, Nikolaidis, A, Nilsonne, G, Niso, G, Norgaard, M, Okell, T, Oostenveld, R, Ort, E, Park, P, Pawlik, M, Pernet, C, Pestilli, F, Petr, J, Phillips, C, Poline, J, Pollonini, L, Raamana, P, Ritter, P, Rizzo, G, Robbins, K, Rockhill, A, Rogers, C, Rokem, A, Rorden, C, Routier, A, Saborit-Torres, J, Salo, T, Schirner, M, Smith, R, Spisak, T, Sprenger, J, Swann, N, Szinte, M, Takerkart, S, Thirion, B, Thomas, A, Torabian, S, Varoquaux, G, Voytek, B, Welzel, J, Wilson, M, Yarkoni, T, Gorgolewski, K, Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L., Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la Iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, Galassi, Anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G., Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Marcantoni, Eleonora, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W., Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, and Gorgolewski, Krzysztof J.

Abstract

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

Published
2024

8. Thickness network features for prognostic applications in dementia

Author

Raamana, Pradeep Reddy, Weiner, Michael W, Wang, Lei, Beg, Mirza Faisal, and Initiative, Alzheimer's Disease Neuroimaging

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Alzheimer's Disease, Acquired Cognitive Impairment, Brain Disorders, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Dementia, Biomedical Imaging, Aging, Prevention, Neurodegenerative, Neurological, Alzheimer Disease, Biomarkers, Cerebral Cortex, Cognitive Dysfunction, Diagnosis, Differential, Early Diagnosis, Humans, Magnetic Resonance Imaging, Neuroimaging, Prognosis, Sensitivity and Specificity, Cortical thickness, Network properties, Fusion, Multiple kernel learning, Early detection, Mild cognitive impairment, Alzheimer, Alzheimer's Disease Neuroimaging Initiative, Clinical Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Regional analysis of cortical thickness has been studied extensively in building imaging biomarkers for early detection of Alzheimer's disease but not its interregional covariation of thickness. We present novel features based on the inter-regional covariation of cortical thickness. Initially, the cortical labels of each subject are partitioned into small patches (graph nodes) by spatial k-means clustering. A graph is then constructed by establishing a link between 2 nodes if the difference in thickness between the nodes is below a certain threshold. From this binary graph, a thickness network is computed using nodal degree, betweenness, and clustering coefficient measures. Fusing them with multiple kernel learning, it is observed that thickness network features discriminate mild cognitive impairment (MCI) converters from controls (CN) with an area under curve (AUC) of 0.83, 74% sensitivity and 76% specificity on a large subset obtained from the Alzheimer's Disease Neuroimaging Initiative data set. A comparison of predictive utility in Alzheimer's disease and/or CN classification (AUC of 0.92, 80% sensitivity [SENS] and 90% specificity [SPEC]), in discriminating CN from MCI (converters and nonconverters combined; AUC of 0.75, SENS and SPEC of 64% and 73%, respectively) and in discriminating between MCI nonconverters and MCI converters (AUC of 0.68, SENS and SPEC of 65% and 64%) is also presented. ThickNet features as defined here are novel, can be derived from a single magnetic resonance imaging scan, and demonstrate the potential for the computer-aided prognostic applications.

Published
2015

11. Three-Class Differential Diagnosis among Alzheimer Disease, Frontotemporal Dementia, and Controls

Author

Raamana, Pradeep Reddy, Rosen, Howard, Miller, Bruce, Weiner, Michael W, Wang, Lei, and Beg, Mirza Faisal

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Frontotemporal Dementia (FTD), Rare Diseases, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Aging, Alzheimer's Disease Related Dementias (ADRD), Acquired Cognitive Impairment, Brain Disorders, Neurodegenerative, Biomedical Imaging, Dementia, 4.1 Discovery and preclinical testing of markers and technologies, 4.2 Evaluation of markers and technologies, Neurological, differential diagnosis, Alzheimer, frontotemporal disease, multi-class, ventricle, Clinical sciences, Biological psychology
Abstract

Biomarkers derived from brain magnetic resonance (MR) imaging have promise in being able to assist in the clinical diagnosis of brain pathologies. These have been used in many studies in which the goal has been to distinguish between pathologies such as Alzheimer's disease and healthy aging. However, other dementias, in particular, frontotemporal dementia, also present overlapping pathological brain morphometry patterns. Hence, a classifier that can discriminate morphometric features from a brain MRI from the three classes of normal aging, Alzheimer's disease (AD), and frontotemporal dementia (FTD) would offer considerable utility in aiding in correct group identification. Compared to the conventional use of multiple pair-wise binary classifiers that learn to discriminate between two classes at each stage, we propose a single three-way classification system that can discriminate between three classes at the same time. We present a novel classifier that is able to perform a three-class discrimination test for discriminating among AD, FTD, and normal controls (NC) using volumes, shape invariants, and local displacements (three features) of hippocampi and lateral ventricles (two structures times two hemispheres individually) obtained from brain MR images. In order to quantify its utility in correct discrimination, we optimize the three-class classifier on a training set and evaluate its performance using a separate test set. This is a novel, first-of-its-kind comparative study of multiple individual biomarkers in a three-class setting. Our results demonstrate that local atrophy features in lateral ventricles offer the potential to be a biomarker in discriminating among AD, FTD, and NC in a three-class setting for individual patient classification.

Published
2014

13. Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA

Author

Sinha, Harsh and Raamana, Pradeep Reddy

Subjects
neuroimaging, quality assurance, dataset integrity, protocol compliance, DICOM, open data
Abstract

The neuroimaging community is steering towards increasingly large and diverse datasets acquired by multisite consortia. Pooling data across diverse sources requires consistency and compliance with the acquisition protocols i.e., ensuring different sites and scanners for a given project have used identical or compatible MR physics parameter values. Conventionally, protocol compliance has been an ad-hoc and manual process that is easily error-prone. Moreover, this is often overlooked for lack of realization that parameter values are routinely improvised locally at various sites in different ways. Ensuring compliance is an arduous process for many reasons, including difficulties in working with the complicated DICOM standard and lack of resources allocated towards protocol compliance and data management. The overlooked inconsistencies across acquisition protocols can reduce SNR, statistical power, and in the worst case, may invalidate the results altogether due to incompatible values. To address this issue, we developed an assistive tool to interface with multiple dataset formats (DICOM, BIDS) and automatically generate protocol compliance reports. In this paper, we describe the origins of the issue and demonstrate its prevalence based on our analysis of the ABCD dataset and, over 20 open neuroimaging datasets. We found that many of these datasets exhibit non-compliance in acquisition parameters. We propose a practical quality assurance (QA) solution to address the issue and offer an open-source tool mrQAto monitor protocol compliance in neuroimaging datasets.

Published
2023
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14. Thickness NETwork (ThickNet) Features for the Detection of Prodromal AD

Author

for The Alzheimer’s Disease Neuroimaging Initiative, Raamana, Pradeep Reddy, Wang, Lei, Beg, Mirza Faisal, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Wu, Guorong, editor, Zhang, Daoqiang, editor, Shen, Dinggang, editor, Yan, Pingkun, editor, Suzuki, Kenji, editor, and Wang, Fei, editor

Published
2013
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15. Visual QC Protocol for FreeSurfer Cortical Parcellations from Anatomical MRI

Author

Raamana, Pradeep Reddy, primary, Theyers, Athena, additional, Selliah, Tharushan, additional, Bhati, Piali, additional, Arnott, Stephen R., additional, Hassel, Stefanie, additional, Nanayakkara, Nuwan D., additional, M. Scott, Christopher J., additional, Harris, Jacqueline, additional, Zamyadi, Mojdeh, additional, Lam, Raymond W., additional, Milev, Roumen, additional, Müller, Daniel J., additional, Rotzinger, Susan, additional, Frey, Benicio N., additional, Kennedy, Sidney H., additional, Black, Sandra E., additional, Lang, Anthony, additional, Masellis, Mario, additional, Symons, Sean, additional, Bartha, Robert, additional, MacQueen, Glenda M., additional, and C. Strother, Stephen, additional

Published
2022
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17. Human Action Recognition in Table-Top Scenarios : An HMM-Based Analysis to Optimize the Performance

Author

Raamana, Pradeep Reddy, Grest, Daniel, Krueger, Volker, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Kropatsch, Walter G., editor, Kampel, Martin, editor, and Hanbury, Allan, editor

Published
2007
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21. Behavioral Markers for Deficits in Speed of Processing in Cerebrovascular Disease

Author

Chen, Ying, primary, Sunderland, Kelly M, additional, Khoo, Yuelee, additional, McLaughlin, Paula M, additional, Kwan, Donna, additional, Fraser, Julia, additional, Ramirez, Joel, additional, Binns, Malcolm A, additional, Arnott, Stephen R, additional, Beaton, Derek, additional, Brien, Donald C, additional, Casaubon, Leanne K, additional, Coe, Brian C, additional, Cornish, Benjamin, additional, Dowlatshahi, Dariush, additional, Hassan, Ayman, additional, Levine, Brian, additional, Lou, Wendy, additional, Mandzia, Jennifer, additional, McIlroy, William, additional, Montero-Odasso, Manuel, additional, Ooteghem, Karen Van, additional, Orange, Joseph B, additional, Peltsch, Alicia J, additional, Pieruccini-Faria, Frederico, additional, Raamana, Pradeep Reddy, additional, Roberts, Angela C, additional, Sahlas, Demetrios, additional, Saposnik, Gustavo, additional, Strother, Stephen C, additional, Swartz, Richard H, additional, Troyer, Angela K, additional, and Munoz, Doug M, additional

Published
2021
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22. Centering inclusivity in the design of online conferences:An OHBM-Open Science perspective

Author

Levitis, Elizabeth, Van Praag, Cassandra D.Gould, Gau, Rémi, Heunis, Stephan, Dupre, Elizabeth, Kiar, Gregory, Bottenhorn, Katherine L., Glatard, Tristan, Nikolaidis, Aki, Whitaker, Kirstie Jane, Mancini, Matteo, Niso, Guiomar, Afyouni, Soroosh, Alonso-Ortiz, Eva, Appelhoff, Stefan, Arnatkeviciute, Aurina, Atay, Selim Melvin, Auer, Tibor, Baracchini, Giulia, Bayer, Johanna M.M., Beauvais, Michael J.S., Bijsterbosch, Janine D., Bilgin, Isil P., Bollmann, Saskia, Bollmann, Steffen, Botvinik-Nezer, Rotem, Bright, Molly G., Calhoun, Vince D., Chen, Xiao, Chopra, Sidhant, Chuan-Peng, Hu, Close, Thomas G., Cookson, Savannah L., Craddock, R. Cameron, De La Vega, Alejandro, De Leener, Benjamin, Demeter, Damion V., Di Maio, Paola, Dickie, Erin W., Eickhoff, Simon B., Esteban, Oscar, Finc, Karolina, Frigo, Matteo, Ganesan, Saampras, Ganz, Melanie, Garner, Kelly G., Garza-Villarreal, Eduardo A., Gonzalez-Escamilla, Gabriel, Goswami, Rohit, Griffiths, John D., Grootswagers, Tijl, Guay, Samuel, Guest, Olivia, Handwerker, Daniel A., Herholz, Peer, Heuer, Katja, Huijser, Dorien C., Iacovella, Vittorio, Joseph, Michael J.E., Karakuzu, Agah, Keator, David B., Kobeleva, Xenia, Kumar, Manoj, Laird, Angela R., Larson-Prior, Linda J., Lautarescu, Alexandra, Lazari, Alberto, Legarreta, Jon Haitz, Li, Xue Ying, Lv, Jinglei, Mansour L., Sina, Meunier, David, Moraczewski, Dustin, Nandi, Tulika, Nastase, Samuel A., Nau, Matthias, Noble, Stephanie, Norgaard, Martin, Obungoloch, Johnes, Oostenveld, Robert, Orchard, Edwina R., Pinho, Ana Luísa, Poldrack, Russell A., Qiu, Anqi, Raamana, Pradeep Reddy, Rokem, Ariel, Rutherford, Saige, Sharan, Malvika, Shaw, Thomas B., Syeda, Warda T., Testerman, Meghan M., Toro, Roberto, Valk, Sofie L., Van Den Bossche, Sofie, Varoquaux, Gaël, Váša, František, Veldsman, Michele, Vohryzek, Jakub, Wagner, Adina S., Walsh, Reubs J., White, Tonya, Wong, Fu Te, Xie, Xihe, Yan, Chao Gan, Yang, Yu Fang, Yee, Yohan, Zanitti, Gaston E., Van Gulick, Ana E., Duff, Eugene, Maumet, Camille, Levitis, Elizabeth, Van Praag, Cassandra D.Gould, Gau, Rémi, Heunis, Stephan, Dupre, Elizabeth, Kiar, Gregory, Bottenhorn, Katherine L., Glatard, Tristan, Nikolaidis, Aki, Whitaker, Kirstie Jane, Mancini, Matteo, Niso, Guiomar, Afyouni, Soroosh, Alonso-Ortiz, Eva, Appelhoff, Stefan, Arnatkeviciute, Aurina, Atay, Selim Melvin, Auer, Tibor, Baracchini, Giulia, Bayer, Johanna M.M., Beauvais, Michael J.S., Bijsterbosch, Janine D., Bilgin, Isil P., Bollmann, Saskia, Bollmann, Steffen, Botvinik-Nezer, Rotem, Bright, Molly G., Calhoun, Vince D., Chen, Xiao, Chopra, Sidhant, Chuan-Peng, Hu, Close, Thomas G., Cookson, Savannah L., Craddock, R. Cameron, De La Vega, Alejandro, De Leener, Benjamin, Demeter, Damion V., Di Maio, Paola, Dickie, Erin W., Eickhoff, Simon B., Esteban, Oscar, Finc, Karolina, Frigo, Matteo, Ganesan, Saampras, Ganz, Melanie, Garner, Kelly G., Garza-Villarreal, Eduardo A., Gonzalez-Escamilla, Gabriel, Goswami, Rohit, Griffiths, John D., Grootswagers, Tijl, Guay, Samuel, Guest, Olivia, Handwerker, Daniel A., Herholz, Peer, Heuer, Katja, Huijser, Dorien C., Iacovella, Vittorio, Joseph, Michael J.E., Karakuzu, Agah, Keator, David B., Kobeleva, Xenia, Kumar, Manoj, Laird, Angela R., Larson-Prior, Linda J., Lautarescu, Alexandra, Lazari, Alberto, Legarreta, Jon Haitz, Li, Xue Ying, Lv, Jinglei, Mansour L., Sina, Meunier, David, Moraczewski, Dustin, Nandi, Tulika, Nastase, Samuel A., Nau, Matthias, Noble, Stephanie, Norgaard, Martin, Obungoloch, Johnes, Oostenveld, Robert, Orchard, Edwina R., Pinho, Ana Luísa, Poldrack, Russell A., Qiu, Anqi, Raamana, Pradeep Reddy, Rokem, Ariel, Rutherford, Saige, Sharan, Malvika, Shaw, Thomas B., Syeda, Warda T., Testerman, Meghan M., Toro, Roberto, Valk, Sofie L., Van Den Bossche, Sofie, Varoquaux, Gaël, Váša, František, Veldsman, Michele, Vohryzek, Jakub, Wagner, Adina S., Walsh, Reubs J., White, Tonya, Wong, Fu Te, Xie, Xihe, Yan, Chao Gan, Yang, Yu Fang, Yee, Yohan, Zanitti, Gaston E., Van Gulick, Ana E., Duff, Eugene, and Maumet, Camille

Abstract

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

Published
2021

23. Cortical Thickness Estimation in Individuals With Cerebral Small Vessel Disease, Focal Atrophy, and Chronic Stroke Lesions

Author

Ozzoude, Miracle, primary, Ramirez, Joel, additional, Raamana, Pradeep Reddy, additional, Holmes, Melissa F., additional, Walker, Kirstin, additional, Scott, Christopher J. M., additional, Gao, Fuqiang, additional, Goubran, Maged, additional, Kwan, Donna, additional, Tartaglia, Maria C., additional, Beaton, Derek, additional, Saposnik, Gustavo, additional, Hassan, Ayman, additional, Lawrence-Dewar, Jane, additional, Dowlatshahi, Dariush, additional, Strother, Stephen C., additional, Symons, Sean, additional, Bartha, Robert, additional, Swartz, Richard H., additional, and Black, Sandra E., additional

Published
2020
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24. Effective Self-Management for Early Career Researchers in the Natural and Life Sciences

Author

Bielczyk, Natalia Z., primary, Ando, Ayaka, additional, Badhwar, AmanPreet, additional, Caldinelli, Chiara, additional, Gao, Mengxia, additional, Haugg, Amelie, additional, Hernandez, Leanna M., additional, Ito, Kaori L., additional, Kessler, Dan, additional, Lurie, Dan, additional, Makary, Meena M., additional, Nikolaidis, Aki, additional, Veldsman, Michele, additional, Allen, Christopher, additional, Bankston, Adriana, additional, Bottenhorn, Katherine L., additional, Braukmann, Ricarda, additional, Calhoun, Vince, additional, Cheplygina, Veronika, additional, Boffino, Catarina Costa, additional, Ercan, Ece, additional, Finc, Karolina, additional, Foo, Heidi, additional, Khatibi, Ali, additional, La, Christian, additional, Mehler, David M.A., additional, Narayanan, Sridar, additional, Poldrack, Russell A., additional, Raamana, Pradeep Reddy, additional, Salo, Taylor, additional, Godard-Sebillotte, Claire, additional, Uddin, Lucina Q., additional, Valeriani, Davide, additional, Valk, Sofie L., additional, Walton, Courtney C., additional, Ward, Phillip G.D., additional, Yanes, Julio A., additional, and Zhou, Xinqi, additional

Published
2020
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28. INFLUENCE OF NETWORK CONSTRUCTION METHODS ON PATH LENGTH VALUES IN ALZHEIMER’S DISEASE: A MULTI-STUDY ANALYSIS OF MRI CONNECTIVITY STUDIES

Author

Dicks, Ellen, He, Yong, Beg, Faisal, Biessels, Geert Jan, Carmeli, Cristian, Chen, Guangyu, Çiftçi, Koray, Dai, Zhengjia, Van Dellen, Edwin, Dyrba, Martin, Friedman, Eric J., de Haan, Willem, Jalili, Mahdi, Jeong, Jaeseung, Jeong, Yong, Jiang, Tianzi, Knyazeva, Maria G., Lee, Dong Young, Li, Shi-Jiang, Liu, Yong, McCarthy, Paul, Rodriguez, Luis Peraza, Phillips, David, Raamana, Pradeep Reddy, Reijmer, Yael D., Seo, Eun Hyun, Sepulcre, Jorge, Soldan, Anja, Suckling, John, Taylor, John-Paul, Teng, Gao-Jun, Wink, Alle Meije, Barkhof, Frederik, Scheltens, Philip, Van der Flier, Wiesje M., Tijms, Betty M., Neurology, Amsterdam Neuroscience - Neurodegeneration, Radiology and nuclear medicine, Amsterdam Neuroscience - Brain Imaging, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam Neuroscience - Neuroinfection & -inflammation, CCA - Cancer biology and immunology, APH - Personalized Medicine, and APH - Methodology

Published
2018
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30. Does size matter? The relationship between predictive power of single-subject morphometric networks to spatial scale and edge weight.

Author

Raamana, Pradeep Reddy and Strother, Stephen C.

Subjects
*MILD cognitive impairment, *ALZHEIMER'S disease, *FEATURE extraction, *MACHINE learning, *DEFINITIONS
Abstract

Network-level analysis based on anatomical, pairwise similarities (e.g., cortical thickness) has been gaining increasing attention recently. However, there has not been a systematic study of the impact of spatial scale and edge definitions on predictive performance, which is necessary to obtain a clear understanding of their relative performance. In this study, we present a histogram-based approach to construct subject-wise weighted networks that enable a principled comparison across different methods of network analysis. We design several weighted networks based on three large publicly available datasets and perform a robust evaluation of their predictive power under four levels of separability. An interesting insight generated is that changes in nodal size (spatial scale) have no significant impact on predictive power among the three classification experiments and two disease cohorts studied, i.e., mild cognitive impairment and Alzheimer's disease from ADNI, and Autism from the ABIDE dataset. We also release an open source python package called graynet to enable others to leverage the novel network feature extraction algorithms presented here. These techniques and toolbox can also be applied to other modalities due to their domain- and feature-agnostic nature) in diverse applications of connectivity research. In addition, the findings from the ADNI dataset are replicated in the AIBL dataset using an open source machine learning tool called neuropredict. [ABSTRACT FROM AUTHOR]

Published
2020
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32. P3‐342: INFLUENCE OF NETWORK CONSTRUCTION METHODS ON PATH LENGTH VALUES IN ALZHEIMER'S DISEASE: A MULTI‐STUDY ANALYSIS OF MRI CONNECTIVITY STUDIES

Author

Dicks, Ellen, primary, He, Yong, additional, Beg, Faisal, additional, Biessels, Geert Jan, additional, Carmeli, Cristian, additional, Chen, Guangyu, additional, Çiftçi, Koray, additional, Dai, Zhengjia, additional, Van Dellen, Edwin, additional, Dyrba, Martin, additional, Friedman, Eric J., additional, de Haan, Willem, additional, Jalili, Mahdi, additional, Jeong, Jaeseung, additional, Jeong, Yong, additional, Jiang, Tianzi, additional, Knyazeva, Maria G., additional, Lee, Dong Young, additional, Li, Shi-Jiang, additional, Liu, Yong, additional, McCarthy, Paul, additional, Rodriguez, Luis Peraza, additional, Phillips, David, additional, Raamana, Pradeep Reddy, additional, Reijmer, Yael D., additional, Seo, Eun Hyun, additional, Sepulcre, Jorge, additional, Soldan, Anja, additional, Suckling, John, additional, Taylor, John-Paul, additional, Teng, Gao-Jun, additional, Wink, Alle Meije, additional, Barkhof, Frederik, additional, Scheltens, Philip, additional, Van der Flier, Wiesje M., additional, and Tijms, Betty M., additional

Published
2018
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33. IC‐P‐032: INFLUENCE OF NETWORK CONSTRUCTION METHODS ON PATH LENGTH VALUES IN ALZHEIMER'S DISEASE: A MULTI‐STUDY ANALYSIS OF MRI CONNECTIVITY STUDIES

Author

Dicks, Ellen, primary, He, Yong, additional, Beg, Faisal, additional, Biessels, Geert Jan, additional, Carmeli, Cristian, additional, Chen, Guangyu, additional, Çiftçi, Koray, additional, Dai, Zhengjia, additional, Van Dellen, Edwin, additional, Dyrba, Martin, additional, Friedman, Eric J., additional, de Haan, Willem, additional, Jalili, Mahdi, additional, Jeong, Jaeseung, additional, Jeong, Yong, additional, Jiang, Tianzi, additional, Knyazeva, Maria G., additional, Lee, Dong Young, additional, Li, Shi-Jiang, additional, Liu, Yong, additional, McCarthy, Paul, additional, Rodriguez, Luis Peraza, additional, Phillips, David, additional, Raamana, Pradeep Reddy, additional, Reijmer, Yael D., additional, Seo, Eun Hyun, additional, Sepulcre, Jorge, additional, Soldan, Anja, additional, Suckling, John, additional, Taylor, John-Paul, additional, Teng, Gao-Jun, additional, Wink, Alle Meije, additional, Barkhof, Frederik, additional, Scheltens, Philip, additional, Van der Flier, Wiesje M., additional, and Tijms, Betty M., additional

Published
2018
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38. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Author

Gorgolewski, Krzysztof J., primary, Alfaro-Almagro, Fidel, additional, Auer, Tibor, additional, Bellec, Pierre, additional, Capotă, Mihai, additional, Chakravarty, M. Mallar, additional, Churchill, Nathan W., additional, Cohen, Alexander Li, additional, Craddock, R. Cameron, additional, Devenyi, Gabriel A., additional, Eklund, Anders, additional, Esteban, Oscar, additional, Flandin, Guillaume, additional, Ghosh, Satrajit S., additional, Guntupalli, J. Swaroop, additional, Jenkinson, Mark, additional, Keshavan, Anisha, additional, Kiar, Gregory, additional, Liem, Franziskus, additional, Raamana, Pradeep Reddy, additional, Raffelt, David, additional, Steele, Christopher J., additional, Quirion, Pierre-Olivier, additional, Smith, Robert E., additional, Strother, Stephen C., additional, Varoquaux, Gaël, additional, Wang, Yida, additional, Yarkoni, Tal, additional, and Poldrack, Russell A., additional

Published
2017
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39. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Author

Gorgolewski, Krzysztof J; https://orcid.org/0000-0003-3321-7583, Alfaro-Almagro, Fidel; https://orcid.org/0000-0002-9133-5951, Auer, Tibor, Bellec, Pierre; https://orcid.org/0000-0002-9111-0699, Capotă, Mihai; https://orcid.org/0000-0002-7323-2393, Chakravarty, M Mallar; https://orcid.org/0000-0002-0759-5508, Churchill, Nathan W, Cohen, Alexander Li; https://orcid.org/0000-0001-6557-5866, Craddock, R Cameron; https://orcid.org/0000-0002-4950-1303, Devenyi, Gabriel A; https://orcid.org/0000-0002-7766-1187, Eklund, Anders; https://orcid.org/0000-0001-7061-7995, Esteban, Oscar; https://orcid.org/0000-0001-8435-6191, Flandin, Guillaume, Ghosh, Satrajit S; https://orcid.org/0000-0002-5312-6729, Guntupalli, J Swaroop, Jenkinson, Mark; https://orcid.org/0000-0001-6043-0166, Keshavan, Anisha; https://orcid.org/0000-0003-3554-043X, Kiar, Gregory; https://orcid.org/0000-0001-8915-496X, Liem, Franziskus; https://orcid.org/0000-0003-0646-4810, Raamana, Pradeep Reddy; https://orcid.org/0000-0003-4662-0558, Raffelt, David, Steele, Christopher J; https://orcid.org/0000-0003-1656-7928, Quirion, Pierre-Olivier, Smith, Robert E, Strother, Stephen C, Varoquaux, Gaël, Wang, Yida; https://orcid.org/0000-0001-8165-840X, Yarkoni, Tal; https://orcid.org/0000-0002-6558-5113, Poldrack, Russell A; https://orcid.org/0000-0001-6755-0259, Gorgolewski, Krzysztof J; https://orcid.org/0000-0003-3321-7583, Alfaro-Almagro, Fidel; https://orcid.org/0000-0002-9133-5951, Auer, Tibor, Bellec, Pierre; https://orcid.org/0000-0002-9111-0699, Capotă, Mihai; https://orcid.org/0000-0002-7323-2393, Chakravarty, M Mallar; https://orcid.org/0000-0002-0759-5508, Churchill, Nathan W, Cohen, Alexander Li; https://orcid.org/0000-0001-6557-5866, Craddock, R Cameron; https://orcid.org/0000-0002-4950-1303, Devenyi, Gabriel A; https://orcid.org/0000-0002-7766-1187, Eklund, Anders; https://orcid.org/0000-0001-7061-7995, Esteban, Oscar; https://orcid.org/0000-0001-8435-6191, Flandin, Guillaume, Ghosh, Satrajit S; https://orcid.org/0000-0002-5312-6729, Guntupalli, J Swaroop, Jenkinson, Mark; https://orcid.org/0000-0001-6043-0166, Keshavan, Anisha; https://orcid.org/0000-0003-3554-043X, Kiar, Gregory; https://orcid.org/0000-0001-8915-496X, Liem, Franziskus; https://orcid.org/0000-0003-0646-4810, Raamana, Pradeep Reddy; https://orcid.org/0000-0003-4662-0558, Raffelt, David, Steele, Christopher J; https://orcid.org/0000-0003-1656-7928, Quirion, Pierre-Olivier, Smith, Robert E, Strother, Stephen C, Varoquaux, Gaël, Wang, Yida; https://orcid.org/0000-0001-8165-840X, Yarkoni, Tal; https://orcid.org/0000-0002-6558-5113, and Poldrack, Russell A; https://orcid.org/0000-0001-6755-0259

Abstract

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.

Published
2017

40. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Author

McGovern Institute for Brain Research at MIT, Ghosh, Satrajit S, Gorgolewski, Krzysztof J., Alfaro-Almagro, Fidel, Auer, Tibor, Bellec, Pierre, Chakravarty, M. Mallar, Churchill, Nathan W., Cohen, Alexander Li, Craddock, R. Cameron, Devenyi, Gabriel A., Eklund, Anders, Esteban, Oscar, Flandin, Guillaume, Ghosh, Satrajit S., Guntupalli, J. Swaroop, Jenkinson, Mark, Keshavan, Anisha, Kiar, Gregory, Liem, Franziskus, Raamana, Pradeep Reddy, Raffelt, David, Steele, Christopher J., Quirion, Pierre-Olivier, Smith, Robert E., Strother, Stephen C., Wang, Yida, Yarkoni, Tal, Poldrack, Russell A., Capota, Mihai, Varoquaux, Gael, McGovern Institute for Brain Research at MIT, Ghosh, Satrajit S, Gorgolewski, Krzysztof J., Alfaro-Almagro, Fidel, Auer, Tibor, Bellec, Pierre, Chakravarty, M. Mallar, Churchill, Nathan W., Cohen, Alexander Li, Craddock, R. Cameron, Devenyi, Gabriel A., Eklund, Anders, Esteban, Oscar, Flandin, Guillaume, Ghosh, Satrajit S., Guntupalli, J. Swaroop, Jenkinson, Mark, Keshavan, Anisha, Kiar, Gregory, Liem, Franziskus, Raamana, Pradeep Reddy, Raffelt, David, Steele, Christopher J., Quirion, Pierre-Olivier, Smith, Robert E., Strother, Stephen C., Wang, Yida, Yarkoni, Tal, Poldrack, Russell A., Capota, Mihai, and Varoquaux, Gael

Abstract

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms., United States. National Institutes of Health (NIH-NIBIB R01 EB020740)

Published
2017

41. BIDS Apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Author

Gorgolewski, Krzysztof J., primary, Alfaro-Almagro, Fidel, additional, Auer, Tibor, additional, Bellec, Pierre, additional, Capotă, Mihai, additional, Chakravarty, M. Mallar, additional, Churchill, Nathan W., additional, Cohen, Alexander Li, additional, Craddock, R. Cameron, additional, Devenyi, Gabriel A., additional, Eklund, Anders, additional, Esteban, Oscar, additional, Flandin, Guillaume, additional, Ghosh, Satrajit S., additional, Guntupalli, J. Swaroop, additional, Jenkinson, Mark, additional, Keshavan, Anisha, additional, Kiar, Gregory, additional, Liem, Franziskus, additional, Raamana, Pradeep Reddy, additional, Raffelt, David, additional, Steele, Christopher J., additional, Quirion, Pierre-Olivier, additional, Smith, Robert E., additional, Strother, Stephen C., additional, Varoquaux, Gaël, additional, Yarkoni, Tal, additional, Wang, Yida, additional, and Poldrack, Russell A., additional

Published
2016
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