Search

Your search keyword '"Poline, J."' showing total 323 results
Start Over Author "Poline, J."
323 results on '"Poline, J."'

1. A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

Author

Abrams, Mathew Birdsall, Bjaalie, Jan G., Das, Samir, Egan, Gary F., Ghosh, Satrajit S., Goscinski, Wojtek J., Grethe, Jeffrey S., Kotaleski, Jeanette Hellgren, Ho, Eric Tatt Wei, Kennedy, David N., Lanyon, Linda J., Leergaard, Trygve B., Mayberg, Helen S., Milanesi, Luciano, Mouček, Roman, Poline, J. B., Roy, Prasun K., Strother, Stephen C., Tang, Tong Boon, Tiesinga, Paul, Wachtler, Thomas, Wójcik, Daniel K., and Martone, Maryann E.

Published
2022
Full Text
View/download PDF

2. 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

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

Author

Poldrack, R. A., Markiewicz, C. J., Appelhoff, S., Ashar, Y. K., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Bertazzoli, G., Bhogawar, S., Blair, R. W., Bortoletto, M., Boudreau, M., Brooks, T. L., Bénar, C. G., Calhoun, V. D., Castelli, F. M., Clement, P., Cohen, A. L., Cohen-Adad, J., Dambrosio, S., Delorme, A., Devinsky, O., Draschkow, D., Duff, E. P., Dupre, E., Earl, E., Esteban, O., Feingold, F. W., Flandin, G., Galassi, A., Gallitto, G., Ganz, M., Gholam, J., Ghosh, S. S., Giacomel, A., Gillman, A. G., Gleeson, P., Gramfort, A., Guay, S., Guidali, G., Halchenko, Y. O., Handwerker, D. A., Hardcastle, N., Herholz, P., Hermes, D., Honey, C. J., Innis, R. B., Ioanas, H.-I., Jahn, A., Karakuzu, A., Keator, D. B., Kiar, G., Kincses, B., Laird, A. R., Lau, J. C., Lazari, A., Legarreta, J. H., Li, A., Li, X., Love, B. C., Lu, H., Maumet, C., Mazzamuto, G., Meisler, S. L., Mikkelsen, M., Mutsaerts, H., Nichols, T. E., Nikolaidis, A., Nilsonne, G., Niso, G., Norgaard, M., Okell, T. W., Oostenveld, R., Ort, E., Park, P. J., Pawlik, M., Pernet, C. R., Pestilli, F., (0000-0002-3201-6002) Petr, J., Phillips, C., Poline, J.-B., Pollonini, L., Raamana, P. R., Ritter, P., Rizzo, G., Robbins, K. A., Rockhill, A. P., Rogers, C., Rokem, A., Rorden, C., Routier, A., Saborit-Torres, J. M., Salo, T., Schirner, M., Smith, R. E., Spisak, T., Sprenger, J., Swann, N. C., Szinte, M., Takerkart, S., Thirion, B., Thomas, A. G., Torabian, S., Varoquaux, G., Vaya, M. D. L. I., Voytek, B., Welzel, J., Wilson, M., Hollander, G., Vega, A., Gorgolewski, K. J., Poldrack, R. A., Markiewicz, C. J., Appelhoff, S., Ashar, Y. K., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Bertazzoli, G., Bhogawar, S., Blair, R. W., Bortoletto, M., Boudreau, M., Brooks, T. L., Bénar, C. G., Calhoun, V. D., Castelli, F. M., Clement, P., Cohen, A. L., Cohen-Adad, J., Dambrosio, S., Delorme, A., Devinsky, O., Draschkow, D., Duff, E. P., Dupre, E., Earl, E., Esteban, O., Feingold, F. W., Flandin, G., Galassi, A., Gallitto, G., Ganz, M., Gholam, J., Ghosh, S. S., Giacomel, A., Gillman, A. G., Gleeson, P., Gramfort, A., Guay, S., Guidali, G., Halchenko, Y. O., Handwerker, D. A., Hardcastle, N., Herholz, P., Hermes, D., Honey, C. J., Innis, R. B., Ioanas, H.-I., Jahn, A., Karakuzu, A., Keator, D. B., Kiar, G., Kincses, B., Laird, A. R., Lau, J. C., Lazari, A., Legarreta, J. H., Li, A., Li, X., Love, B. C., Lu, H., Maumet, C., Mazzamuto, G., Meisler, S. L., Mikkelsen, M., Mutsaerts, H., Nichols, T. E., Nikolaidis, A., Nilsonne, G., Niso, G., Norgaard, M., Okell, T. W., Oostenveld, R., Ort, E., Park, P. J., Pawlik, M., Pernet, C. R., Pestilli, F., (0000-0002-3201-6002) Petr, J., Phillips, C., Poline, J.-B., Pollonini, L., Raamana, P. R., Ritter, P., Rizzo, G., Robbins, K. A., Rockhill, A. P., Rogers, C., Rokem, A., Rorden, C., Routier, A., Saborit-Torres, J. M., Salo, T., Schirner, M., Smith, R. E., Spisak, T., Sprenger, J., Swann, N. C., Szinte, M., Takerkart, S., Thirion, B., Thomas, A. G., Torabian, S., Varoquaux, G., Vaya, M. D. L. I., Voytek, B., Welzel, J., Wilson, M., Hollander, G., Vega, A., and Gorgolewski, K. 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, and the mechanisms by which it has been extended. 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

4. A group model for stable multi-subject ICA on fMRI datasets

Author

Varoquaux, G., Sadaghiani, S., Pinel, P., Kleinschmidt, A., Poline, J. B., and Thirion, B.

Subjects
Statistics - Applications, Statistics - Methodology
Abstract

Spatial Independent Component Analysis (ICA) is an increasingly used data-driven method to analyze functional Magnetic Resonance Imaging (fMRI) data. To date, it has been used to extract sets of mutually correlated brain regions without prior information on the time course of these regions. Some of these sets of regions, interpreted as functional networks, have recently been used to provide markers of brain diseases and open the road to paradigm-free population comparisons. Such group studies raise the question of modeling subject variability within ICA: how can the patterns representative of a group be modeled and estimated via ICA for reliable inter-group comparisons? In this paper, we propose a hierarchical model for patterns in multi-subject fMRI datasets, akin to mixed-effect group models used in linear-model-based analysis. We introduce an estimation procedure, CanICA (Canonical ICA), based on i) probabilistic dimension reduction of the individual data, ii) canonical correlation analysis to identify a data subspace common to the group iii) ICA-based pattern extraction. In addition, we introduce a procedure based on cross-validation to quantify the stability of ICA patterns at the level of the group. We compare our method with state-of-the-art multi-subject fMRI ICA methods and show that the features extracted using our procedure are more reproducible at the group level on two datasets of 12 healthy controls: a resting-state and a functional localizer study.

Published
2010
Full Text
View/download PDF

5. Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

Author

Abrams, Mathew Birdsall, Bjaalie, Jan G., Das, Samir, Egan, Gary F., Ghosh, Satrajit S., Goscinski, Wojtek J., Grethe, Jeffrey S., Kotaleski, Jeanette Hellgren, Ho, Eric Tatt Wei, Kennedy, David N., Lanyon, Linda J., Leergaard, Trygve B., Mayberg, Helen S., Milanesi, Luciano, Mouček, Roman, Poline, J. B., Roy, Prasun K., Strother, Stephen C., Tang, Tong Boon, Tiesinga, Paul, Wachtler, Thomas, Wójcik, Daniel K., and Martone, Maryann E.

Published
2022
Full Text
View/download PDF

8. MR Diffusion-Based Inference of a Fiber Bundle Model from a Population of Subjects

Author

El Kouby, V., Cointepas, Y., Poupon, C., Rivière, D., Golestani, N., Poline, J. -B., Le Bihan, D., Mangin, J. -F., 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, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Duncan, James S., editor, and Gerig, Guido, editor

Published
2005
Full Text
View/download PDF

10. Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

Author

McGovern Institute for Brain Research at MIT, Abrams, Mathew B., Bjaalie, Jan G., Das, Samir, Egan, Gary F., Ghosh, Satrajit S., Goscinski, Wojtek J., Grethe, Jeffrey S., Kotaleski, Jeanette H., Ho, Eric T. W., Kennedy, David N., Lanyon, Linda J., Leergaard, Trygve B., Mayberg, Helen S., Milanesi, Luciano, Mouček, Roman, Poline, J. B., Roy, Prasun K., Strother, Stephen C., Tang, Tong B., Tiesinga, Paul, McGovern Institute for Brain Research at MIT, Abrams, Mathew B., Bjaalie, Jan G., Das, Samir, Egan, Gary F., Ghosh, Satrajit S., Goscinski, Wojtek J., Grethe, Jeffrey S., Kotaleski, Jeanette H., Ho, Eric T. W., Kennedy, David N., Lanyon, Linda J., Leergaard, Trygve B., Mayberg, Helen S., Milanesi, Luciano, Mouček, Roman, Poline, J. B., Roy, Prasun K., Strother, Stephen C., Tang, Tong B., and Tiesinga, Paul

Abstract

A Correction to this paper has been published: https://doi.org/10.1007/s12021-021-09522-x

Published
2022

11. Genomic architecture of human neuroanatomical diversity

Author

Toro, R, Poline, J-B, Huguet, G, Loth, E, Frouin, V, Banaschewski, T, Barker, G J, Bokde, A, Büchel, C, Carvalho, F M, Conrod, P, Fauth-Bühler, M, Flor, H, Gallinat, J, Garavan, H, Gowland, P, Heinz, A, Ittermann, B, Lawrence, C, Lemaître, H, Mann, K, Nees, F, Paus, T, Pausova, Z, Rietschel, M, Robbins, T, Smolka, M N, Ströhle, A, Schumann, G, and Bourgeron, T

Published
2015
Full Text
View/download PDF

12. Boys do it the right way: Sex-dependent amygdala lateralization during face processing in adolescents

Author

Schneider, S., Peters, J., Bromberg, U., Brassen, S., Menz, M.M., Miedl, S.F., Loth, E., Banaschewski, T., Barbot, A., Barker, G., Conrod, P.J., Dalley, J.W., Flor, H., Gallinat, J., Garavan, H., Heinz, A., Itterman, B., Mallik, C., Mann, K., Artiges, Eric, Paus, T., Poline, J.-B., Rietschel, M., Reed, L., Smolka, M.N., Spanagel, R., Speiser, C., Ströhle, A., Struve, M., Schumann, G., and Büchel, C.

Published
2011
Full Text
View/download PDF

15. Resilience and corpus callosum microstructure in adolescence

Author

Galinowski, A., Miranda, R., Lemaitre, H., Paillère Martinot, M.-L., Artiges, E., Vulser, H., Goodman, R., Penttilä, J., Struve, M., Barbot, A., Fadai, T., Poustka, L., Conrod, P., Banaschewski, T., Barker, G. J., Bokde, A., Bromberg, U., Büchel, C., Flor, H., Gallinat, J., Garavan, H., Heinz, A., Ittermann, B., Kappel, V., Lawrence, C., Loth, E., Mann, K., Nees, F., Paus, T., Pausova, Z., Poline, J.-B., Rietschel, M., Robbins, T. W., Smolka, M., Schumann, G., and Martinot, J.-L.

Published
2015
Full Text
View/download PDF

16. Single nucleotide polymorphism in the neuroplastin locus associates with cortical thickness and intellectual ability in adolescents

Author

Desrivières, S, Lourdusamy, A, Tao, C, Toro, R, Jia, T, Loth, E, Medina, L M, Kepa, A, Fernandes, A, Ruggeri, B, Carvalho, F M, Cocks, G, Banaschewski, T, Barker, G J, Bokde, A LW, Büchel, C, Conrod, P J, Flor, H, Heinz, A, Gallinat, J, Garavan, H, Gowland, P, Brühl, R, Lawrence, C, Mann, K, Martinot, M LP, Nees, F, Lathrop, M, Poline, J-B, Rietschel, M, Thompson, P, Fauth-Bühler, M, Smolka, M N, Pausova, Z, Paus, T, Feng, J, and Schumann, G

Published
2015
Full Text
View/download PDF

17. A Standards Organization for Open and FAIR Neuroscience : the International Neuroinformatics Coordinating Facility

Author

Abrams, M. B., Bjaalie, J. G., Das, S., Egan, G. F., Ghosh, S. S., Goscinski, W. J., Grethe, J. S., Hellgren Kotaleski, Jeanette, Ho, E. T. W., Kennedy, D. N., Lanyon, L. J., Leergaard, T. B., Mayberg, H. S., Milanesi, L., Mouček, R., Poline, J. B., Roy, P. K., Strother, S. C., Tang, T. B., Tiesinga, P., Wachtler, T., Wójcik, D. K., Martone, M. E., Abrams, M. B., Bjaalie, J. G., Das, S., Egan, G. F., Ghosh, S. S., Goscinski, W. J., Grethe, J. S., Hellgren Kotaleski, Jeanette, Ho, E. T. W., Kennedy, D. N., Lanyon, L. J., Leergaard, T. B., Mayberg, H. S., Milanesi, L., Mouček, R., Poline, J. B., Roy, P. K., Strother, S. C., Tang, T. B., Tiesinga, P., Wachtler, T., Wójcik, D. K., and Martone, M. E.

Abstract

There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body., Correction in: Neuroinformatics (2021). DOI: 10.1007/s12021-020-09509-0, WOS: 000639794100001, QC 20220928

Published
2021
Full Text
View/download PDF

20. Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

Author

Abrams, Mathew Birdsall, primary, Bjaalie, Jan G., additional, Das, Samir, additional, Egan, Gary F., additional, Ghosh, Satrajit S., additional, Goscinski, Wojtek J., additional, Grethe, Jeffrey S., additional, Kotaleski, Jeanette Hellgren, additional, Ho, Eric Tatt Wei, additional, Kennedy, David N., additional, Lanyon, Linda J., additional, Leergaard, Trygve B., additional, Mayberg, Helen S., additional, Milanesi, Luciano, additional, Mouček, Roman, additional, Poline, J. B., additional, Roy, Prasun K., additional, Strother, Stephen C., additional, Tang, Tong Boon, additional, Tiesinga, Paul, additional, Wachtler, Thomas, additional, Wójcik, Daniel K., additional, and Martone, Maryann E., additional

Published
2021
Full Text
View/download PDF

21. The DataLad Handbook: A user-focused and workflow-based addition to standard software documentation

Author

Wagner, Adina S., Waite, Laura K., Waite, Alexander Q., Reuter, Nils, Poldrack, Benjamin, Poline, J.-B., Kadelka, Tobias, Markiewicz, Christopher J., Vavra, Peter, Paas, Lya K., Herholz, Peer, Mochalski, Lisa N., Kraljevic, Nevena, Heckner, Marisa K., Halchenko, Yaroslav O., and Hanke, Michael

Subjects
DataLad, Handbook, Software documentation
Abstract

A poster presented at the Organization for Human Brain Mapping (OHBM) conference 2020. The submission abstract was: Big data has arrived in neuroscience: There is growing awareness of the role of sample size and replicable results (Button et al., 2013; Turner et al., 2018), a rise of platforms, tools, and standards that aim to facilitate data sharing and management (Wiener et al., 2016), and unprecedented sample sizes (e.g., UKBiobank; Bzdok & Yeo, 2017). Together with increasingly complex data analyses, it requires methodological knowledge, but also skills in data and software management, to put open, reproducible, and scalable neuroimaging research into effect. Researchers, planners (PIs or funders), and trainers in neuroscience alike are challenged by these demands (Fothergill et al., 2019, Grisham et al., 2016) and rely on documentation of their tools. Researchers need accessible educational content to understand and use a tool, planners need high-level, non-technical information in order to make informed yet efficient decisions on whether a tool fulfils their needs, and trainers need reliable, open teaching material. But without a computer science background, many neuroscientists receive no formal training in data management. To be broadly accessible, documentation needs to cultivate confidence in users regardless of their background. However, software documentation can be suboptimal for novices: It may be incomplete, narrowly focused on individual commands, or assume existing knowledge novices lack (Segal, 2007; Pawlik et al., 2015), and can thereby discourage potential users or inhibit the adoption of valuable tools. DataLad (Halchenko, Hanke et al., 2019) is an open source data management multi-tool that facilitates digital workflows of data and science. It is used as an infrastructure component or utility in a growing number of services and tools (e.g., OpenNeuro, CBRAIN platform, HeuDiConv, brainlife.io). Despite being accessible (free, open, with support for all major OSs) and comprehensive, adoption among users is impeded by a lack of workflow-based and user-focused educational materials. Methods A user-driven alternative to scientific software documentation by software developers, “Documentation Crowdsourcing”, has been successfully employed by the NumPy project (Oliphant, 2006; Pawlik et al., 2015). Extending this concept beyond documentation, we have created the DataLad handbook (handbook.datalad.org) as a free & open-source, user-driven and -focused educational instrument and resource for trainers, users, and planners for (research) data management, independent of their background and skill level. The handbook contains three components: ‘The Basics’, a course-like, continuous narrative that integrates basic functions and concepts into larger workflows as a ‘code-along’ crash course serves as a tutorial. Recipe-like step-by-step how-to-guides (‘use cases’) show high-level overviews for specific applications. Expandable sections contain background information and serve as explanations. The code is tested automatically to ensure correct operation, and the comprehensibility of contents is tested and improved via handbook-based teaching sessions for data management novices (various career stages, MSc students up to PI-level). Slides and automatic code demos can be semi-automatically extracted as readily available, tested resources for teachers. Results The handbook serves several needs: 1) learning-oriented and lesson-like tutorials allow novices to get started, 2) goal-oriented how-to-guides show planners how to solve specific problems, 3) optional explanations provide background and context beyond what is necessary to use a concept or command, and 4) a continuously tested codebase allows trainers to get reliable teaching materials with reproducible examples. Conclusions We present an accessible, free, and open source educational instrument to explain and demonstrate state-of-the-art data management procedures with DataLad. The framework behind the project is generic, and could be reused for similar training materials. The sources can be found at https://github.com/datalad-handbook/book/blob/main/artwork

Published
2020
Full Text
View/download PDF

22. A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

Author

Abrams, Mathew Birdsall, primary, Bjaalie, Jan G., additional, Das, Samir, additional, Egan, Gary F., additional, Ghosh, Satrajit S., additional, Goscinski, Wojtek J., additional, Grethe, Jeffrey S., additional, Kotaleski, Jeanette Hellgren, additional, Ho, Eric Tatt Wei, additional, Kennedy, David N., additional, Lanyon, Linda J., additional, Leergaard, Trygve B., additional, Mayberg, Helen S., additional, Milanesi, Luciano, additional, Mouček, Roman, additional, Poline, J. B., additional, Roy, Prasun K., additional, Strother, Stephen C., additional, Tang, Tong Boon, additional, Tiesinga, Paul, additional, Wachtler, Thomas, additional, Wójcik, Daniel K., additional, and Martone, Maryann E., additional

Published
2021
Full Text
View/download PDF

24. A primal sketch of the cortex mean curvature: a morphogenesis based approach to study the variability of the folding patterns

Author

Cachia, A., Mangin, J.-F., Riviere, D., Kherif, F., Boddaert, N., Andrade, A., Papadopoulos-Orfanos, D., Poline, J.-B., Bloch, I., Zilbovicius, M., Sonigo, P., Brunelle, F., and Regis, J.

Subjects
Human biology -- Research, Business, Electronics, Electronics and electrical industries, Health care industry
Abstract

In this paper, we propose a new representation of the cortical surface that may be used to study the cortex folding process and to recover some putative stable anatomical landmarks called sulcal roots usually buried in the depth of adult brains. This representation is a primal sketch derived from a scale space computed for the mean curvature of the cortical surface. This scale-space stems from a diffusion equation geodesic to the cortical surface. The primal sketch is made up of objects defined from mean curvature minima and saddle points. The resulting sketch aims first at highlighting significant elementary cortical folds, second at representing the fold merging process during brain growth. The relevance of the framework is illustrated by the study of central sulcus sulcal roots from antenatal to adult age. Some results are proposed for ten different brains. Some preliminary results are also provided for superior temporal sulcus. Index Terms--Morphometry, spatial normalization, sulcogenesis, variability.

Published
2003

26. Bilateral hemispheric alteration of memory processes in right medial temporal lobe epilepsy. (Paper)

Author

Dupont, S., Samson, Y., Moortele, P-F Van de, Samson, S., Poline, J-B, Hasboun, D., Bihan, D. Le, and Baulac, M.

Subjects
Hippocampus (Brain) -- Psychological aspects -- Physiological aspects, Memory, Disorders of -- Risk factors, Temporal lobe epilepsy -- Psychological aspects -- Risk factors, Verbal ability -- Physiological aspects -- Psychological aspects, Health, Psychology and mental health, Psychological aspects, Physiological aspects, Risk factors
Abstract

Objective: Functional MRI (fMRI) was used to investigate right medial temporal lobe epilepsy (RTLE) effects on verbal memory. Methods: BOLD fMRI data were collected from seven right sided MTLE patients [...]

Published
2002

37. A Mean Curvature Based Primal Sketch to Study the Cortical Folding Process from Antenatal to Adult Brain

Author

Cachia, A., primary, Mangin, J. -F., additional, Rivière, D., additional, Boddaert, N., additional, Andrade, A., additional, Kherif, F., additional, Sonigo, P., additional, Papadopoulos-Orfanos, D., additional, Zil bovicius, M., additional, Poline, J. -B., additional, Bloch, I., additional, Brunelle, F., additional, and Régis, J., additional

Published
2001
Full Text
View/download PDF

39. Brain status modeling with non-negative projective dictionary learning

Author

Zhang, M. (Mingli), Desrosiers, C. (Christian), Guo, Y. (Yuhong), Khundrakpam, B. (Budhachandra), Al-Sharif, N. (Noor), Kiar, G. (Greg), Valdes-Sosa, P. (Pedro), Poline, J.-B. (Jean-Baptiste), Evans, A. (Alan), Zhang, M. (Mingli), Desrosiers, C. (Christian), Guo, Y. (Yuhong), Khundrakpam, B. (Budhachandra), Al-Sharif, N. (Noor), Kiar, G. (Greg), Valdes-Sosa, P. (Pedro), Poline, J.-B. (Jean-Baptiste), and Evans, A. (Alan)

Abstract

Accurate prediction of individuals’ brain age is critical to establish a baseline for normal brain development. This study proposes to model brain development with a novel non-negative projective dictionary learning (NPDL) approach, which learns a discriminative representation of multi-modal neuroimaging data for predicting brain age. Our approach encodes the variability of subjects in different age groups using separate dictionaries, projecting features into a low-dimensional manifold such that information is preserved only for the corresponding age group. The proposed framework improves upon previous discriminative dictionary learning methods by inco

Published
2019
Full Text
View/download PDF

44. Contributors

Author

Adam, M., primary, Alpert, Nathaniel M., additional, Anderson, J.R., additional, Andreasen, Nancy C., additional, Antonini, A., additional, Ardekani, Babak A., additional, Arndt, Stephan, additional, Ashburner, John, additional, Ashworth, Sharon, additional, Bailey, Dale L., additional, Baker, E., additional, Barnes, D.G., additional, Bench, C., additional, Bendriem, B., additional, Berdichevsky, D., additional, Biegon, A., additional, Blair, R.C., additional, Blomqvist, G., additional, Bloomfield, Peter M., additional, Ponto, Laura L. Boles, additional, Brakeman, Paul, additional, Braun, Michael, additional, Brooks, David J., additional, Brown, C.K., additional, Brown, W.D., additional, Bruckbauer, T., additional, Buckley, K.R., additional, Calonder, C., additional, Campbell, Gregory, additional, Carson, Richard E., additional, Chaly, Thomas, additional, Chan, G. L-Y., additional, Chen, Chin-Tu, additional, Cizadlo, Ted, additional, Cliffe, I.A., additional, Collins, D.L., additional, Cooper, Malcolm, additional, Crivello, F., additional, Crossnoe, M., additional, Cumming, Paul, additional, Cunningham, Vincent J., additional, Czernin, J., additional, Dahlbom, M., additional, Damasio, H., additional, DaSilva, J., additional, Witherspoon, Margaret E. Daube-, additional, DeJesus, O.T., additional, Delforge, J., additional, Dhawan, Vijay, additional, Dickhoven, S., additional, Diksic, Mirko, additional, Eberl, Stefan, additional, Egan, G.F., additional, Eidelberg, David, additional, Eriksson, Lars, additional, Evans, Alan C., additional, Fink, G.R., additional, Fischman, Alan J., additional, Fisher, Ronald E., additional, Fletcher, A., additional, Fontaine, A., additional, Ford, I., additional, Forse, G., additional, Frackowiak, R.S.J., additional, Frank, R.J., additional, Friston, K.J., additional, Frost, J. James, additional, Frouin, V., additional, Fujita, Hideaki, additional, Fujiwara, Takehiko, additional, Fukuda, H., additional, Fulham, Michael J., additional, Gee, Anthony D., additional, Gillings, N., additional, Gjedde, Albert, additional, Glaser, Robert, additional, Grabowski, T.J., additional, Graf, R., additional, Grafton, S.T., additional, Graham, Michael M., additional, Grasby, P., additional, Gunn, R.N., additional, Günther, I., additional, Hagisawa, S., additional, Haida, A., additional, Halber, M., additional, Hallett, Mark, additional, Hansen, Lars K., additional, Harris, Greg, additional, Haslam, Jane, additional, Hasselbalch, Steen, additional, Hatazawa, Jun, additional, Heiss, W.-D., additional, Herholz, K., additional, Herscovitch, Peter, additional, Herzog, H., additional, Hichwa, Richard D., additional, Hoh, C., additional, Holden, J.E., additional, Holm, Søren, additional, Holmes, A.P., additional, Holmes, C.J., additional, Hooper, Patrick K., additional, Houle, S., additional, Houser, D., additional, Huang, Sung-Cheng, additional, Hume, S.P., additional, Hurtig, Richard R., additional, Hussey, D., additional, Hutton, Brian F., additional, Iacoboni, M., additional, Ido, T., additional, Iida, Hidehiro, additional, Inoue, O., additional, Ishii, Kazunari, additional, Ishikawa, Tatsuya, additional, Itoh, H., additional, Itoh, Masatoshi, additional, Iwata, R., additional, Jadali, F., additional, Jagust, W., additional, Jivan, S., additional, Joliot, M., additional, Jones, A.K.P., additional, Jones, C., additional, Jones, Terry, additional, Kanno, Iwao, additional, Kao, Chien-Min, additional, Kapur, S., additional, Karbe, H., additional, Kessler, J., additional, Kilbourn, Michael R., additional, Kimura, Yuichi, additional, Kinahan, P.E., additional, Knorr, U., additional, Kobayashi, K., additional, Kops, E. Rota, additional, Kosugi, Yukio, additional, Kruger, Mark, additional, Kuwabara, Hiroto, additional, Lammertsma, Adriaan A., additional, Laurier, L., additional, Law, Ian, additional, Leenders, K.L., additional, Legg, B., additional, Levin, Z., additional, Lin, Kang-Ping, additional, Links, Jonathan M., additional, Lipinski, B., additional, Lopresti, B.J., additional, Löttgen, J., additional, Luthra, S.K., additional, Ma, Yilong, additional, Maguire, R.P., additional, Mahmood, K., additional, Malizia, Andrea L., additional, Mankoff, David A., additional, Marenco, Stefano, additional, Marrett, S., additional, Mathis, C.A., additional, Matsumura, Y., additional, Mazoyer, B., additional, Mazziotta, John C., additional, McCarron, J.A., additional, Meguro, K., additional, Meikle, Steven R., additional, Mejia, Marco A., additional, Mellet, E., additional, Meltzer, Carolyn Cidis, additional, Meyer, Ernst, additional, Millet, P., additional, Minoshima, S., additional, Mintun, M.A., additional, Missimer, J., additional, Miura, Shuichi, additional, Miyake, M., additional, Momose, Toshimitsu, additional, Mørch, Niels, additional, Morris, Evan D., additional, Morrish, Paul K., additional, Morrison, S., additional, Müller-Gärtner, H.W., additional, Murase, Kenya, additional, Muzi, Mark, additional, Myers, R., additional, Nakamura, Takashi, additional, Nariai, Tadashi, additional, Neelin, P., additional, Nickles, R.J., additional, Nishikawa, Junichi, additional, Nishizawa, Sadahiko, additional, Nutt, D.J., additional, O'Keefe, G.J., additional, O'Leary, Daniel S., additional, O'Sullivan, B.T., additional, O'Sullivan, Finbarr, additional, Oberschelp, W., additional, Ogawa, Toshihide, additional, Ono, S., additional, Osman, S., additional, Patlak, Clifford, additional, Paulson, Olaf B., additional, Pawlik, Gunter, additional, Petit, L., additional, Pietrzyk, U., additional, Pike, V.W., additional, Poline, J.-B., additional, Poole, K., additional, Price, J.C., additional, Psylla, M., additional, Pyzalski, Robert, additional, Rajeswaran, S., additional, Rakshi, James S., additional, Ranicar, Alex, additional, Rauch, Scott L., additional, Remy, P., additional, Reutens, David C., additional, Roberts, Andy, additional, Rosenqvist, G., additional, Rottenberg, D.A., additional, Rousset, Olivier G., additional, Ruth, T.J., additional, Sadato, Norihiro, additional, Samson, Y., additional, Sasaki, H., additional, Sase, Mikiya, additional, Sashin, D., additional, Schaper, K., additional, Schlaug, G., additional, Schnorr, L., additional, Seitz, R.J., additional, Senda, Michio, additional, Shelton, S.E., additional, Shields, Anthony F., additional, Shimosegawa, Eku, additional, Shiraishi, Masahiro, additional, Shrager, Richard, additional, Sidtis, J.J., additional, Simpson, N.R., additional, Smith, D., additional, Smith, Donald F., additional, Snow, B.J., additional, Snyder, Abraham Z., additional, Sossi, V., additional, Spelle, L., additional, Spence, Alexander, additional, Strother, S.C., additional, Stumpf, Martin J., additional, Suganami, Yusuke, additional, Svarer, Claus, additional, Swerdloff, S.J., additional, Syrota, A., additional, Taguchi, A., additional, Talarico, E., additional, Taylor, Chris, additional, Tellman, L., additional, Thiel, A., additional, Danguy, H. J. Tochon-, additional, Toga, Arthur W., additional, Toussaint, P.-J., additional, Townsend, D.W., additional, Toyama, Hinako, additional, Trébossen, R., additional, Tzourio, N., additional, Uchiyama, A., additional, Uemura, Kazuo, additional, Uno, H., additional, Vafaee, M., additional, Vingerhoets, F.J.G., additional, Vontobel, P., additional, Wagner, R., additional, Watabe, Hiroshi, additional, Watkins, G. Leonard, additional, Watson, J.D.G., additional, Wernick, Miles, additional, Wienhard, K., additional, Wilson, A.A., additional, Wilson, S., additional, Wollenweber, Scott D., additional, Wong, Dean F., additional, Woods, Roger P., additional, Worsley, K.J., additional, Yan, Yuchen, additional, Yanai, K., additional, Yang, J., additional, Yap, Jeffrey T., additional, Yu, D.C., additional, Zeien, Gene, additional, Zhou, Y., additional, and Zubieta, Jon Kar, additional

Published
1996
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results