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The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.

Scientific data

Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, Poline JB, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA.
PMID: 27326542
Sci Data. 2016 Jun 21;3:160044. doi: 10.1038/sdata.2016.44.

The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain....

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Gorgolewski KJ, Auer T, Calhoun VD, et al. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data. 2016;3:160044doi: 10.1038/sdata.2016.44.
Gorgolewski, K. J., Auer, T., Calhoun, V. D., Craddock, R. C., Das, S., Duff, E. P., Flandin, G., Ghosh, S. S., Glatard, T., Halchenko, Y. O., Handwerker, D. A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B. N., Nichols, T. E., Pellman, J., Poline, J. B., Rokem, A., Schaefer, G., Sochat, V., Triplett, W., Turner, J. A., Varoquaux, G., & Poldrack, R. A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific data, 3160044. https://doi.org/10.1038/sdata.2016.44
Gorgolewski, Krzysztof J, et al. "The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments." Scientific data vol. 3 (2016): 160044. doi: https://doi.org/10.1038/sdata.2016.44
Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, Poline JB, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data. 2016 Jun 21;3:160044. doi: 10.1038/sdata.2016.44. PMID: 27326542; PMCID: PMC4978148.
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PyXNAT: XNAT in Python.

Frontiers in neuroinformatics

Schwartz Y, Barbot A, Thyreau B, Frouin V, Varoquaux G, Siram A, Marcus DS, Poline JB.
PMID: 22654752
Front Neuroinform. 2012 May 24;6:12. doi: 10.3389/fninf.2012.00012. eCollection 2012.

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to...

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Schwartz Y, Barbot A, Thyreau B, et al. PyXNAT: XNAT in Python. Front Neuroinform. 2012;6:12doi: 10.3389/fninf.2012.00012.
Schwartz, Y., Barbot, A., Thyreau, B., Frouin, V., Varoquaux, G., Siram, A., Marcus, D. S., & Poline, J. B. (2012). PyXNAT: XNAT in Python. Frontiers in neuroinformatics, 612. https://doi.org/10.3389/fninf.2012.00012
Schwartz, Yannick, et al. "PyXNAT: XNAT in Python." Frontiers in neuroinformatics vol. 6 (2012): 12. doi: https://doi.org/10.3389/fninf.2012.00012
Schwartz Y, Barbot A, Thyreau B, Frouin V, Varoquaux G, Siram A, Marcus DS, Poline JB. PyXNAT: XNAT in Python. Front Neuroinform. 2012 May 24;6:12. doi: 10.3389/fninf.2012.00012. eCollection 2012. PMID: 22654752; PMCID: PMC3354345.
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Josephson effect and quantum phase slippage in superfluids.

Physical review letters

Avenel O, Varoquaux E.
PMID: 10038541
Phys Rev Lett. 1988 Feb 01;60(5):416-419. doi: 10.1103/PhysRevLett.60.416.

No abstract available.

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Avenel O, Varoquaux E. Josephson effect and quantum phase slippage in superfluids. Phys Rev Lett. 1988;60(5):416-419doi: 10.1103/PhysRevLett.60.416.
Avenel, O., & Varoquaux, E. (1988). Josephson effect and quantum phase slippage in superfluids. Physical review letters, 60(5), 416-419. https://doi.org/10.1103/PhysRevLett.60.416
Avenel, and Varoquaux. "Josephson effect and quantum phase slippage in superfluids." Physical review letters vol. 60,5 (1988): 416-419. doi: https://doi.org/10.1103/PhysRevLett.60.416
Avenel O, Varoquaux E. Josephson effect and quantum phase slippage in superfluids. Phys Rev Lett. 1988 Feb 01;60(5):416-419. doi: 10.1103/PhysRevLett.60.416. PMID: 10038541.
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Splitting of the squashing collective mode of superfluid 3He-B by a magnetic field.

Physical review letters

Kim N, Lee DM, Movshovich R, Varoquaux E.
PMID: 10038882
Phys Rev Lett. 1988 Oct 10;61(15):1732-1735. doi: 10.1103/PhysRevLett.61.1732.

No abstract available.

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Kim N, Lee DM, Movshovich R, et al. Splitting of the squashing collective mode of superfluid 3He-B by a magnetic field. Phys Rev Lett. 1988;61(15):1732-1735doi: 10.1103/PhysRevLett.61.1732.
Kim, N., Lee, D. M., Movshovich, R., & Varoquaux, E. (1988). Splitting of the squashing collective mode of superfluid 3He-B by a magnetic field. Physical review letters, 61(15), 1732-1735. https://doi.org/10.1103/PhysRevLett.61.1732
Kim, et al. "Splitting of the squashing collective mode of superfluid 3He-B by a magnetic field." Physical review letters vol. 61,15 (1988): 1732-1735. doi: https://doi.org/10.1103/PhysRevLett.61.1732
Kim N, Lee DM, Movshovich R, Varoquaux E. Splitting of the squashing collective mode of superfluid 3He-B by a magnetic field. Phys Rev Lett. 1988 Oct 10;61(15):1732-1735. doi: 10.1103/PhysRevLett.61.1732. PMID: 10038882.
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Nonlinear transmission of zero sound in superfluid 3He-A: A saturation of the pair-breaking attenuation mechanism.

Physical review letters

Avenel O, Combescot R, Maki K, Piché L, Rouff M, Varoquaux E.
PMID: 10031024
Phys Rev Lett. 1985 Apr 01;54(13):1408-1411. doi: 10.1103/PhysRevLett.54.1408.

No abstract available.

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Avenel O, Combescot R, Maki K, et al. Nonlinear transmission of zero sound in superfluid 3He-A: A saturation of the pair-breaking attenuation mechanism. Phys Rev Lett. 1985;54(13):1408-1411doi: 10.1103/PhysRevLett.54.1408.
Avenel, O., Combescot, R., Maki, K., Piché, L., Rouff, M., & Varoquaux, E. (1985). Nonlinear transmission of zero sound in superfluid 3He-A: A saturation of the pair-breaking attenuation mechanism. Physical review letters, 54(13), 1408-1411. https://doi.org/10.1103/PhysRevLett.54.1408
Avenel, et al. "Nonlinear transmission of zero sound in superfluid 3He-A: A saturation of the pair-breaking attenuation mechanism." Physical review letters vol. 54,13 (1985): 1408-1411. doi: https://doi.org/10.1103/PhysRevLett.54.1408
Avenel O, Combescot R, Maki K, Piché L, Rouff M, Varoquaux E. Nonlinear transmission of zero sound in superfluid 3He-A: A saturation of the pair-breaking attenuation mechanism. Phys Rev Lett. 1985 Apr 01;54(13):1408-1411. doi: 10.1103/PhysRevLett.54.1408. PMID: 10031024.
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Inter-subject Registration of Functional Images: Do We Need Anatomical Images?.

Frontiers in neuroscience

Dohmatob E, Varoquaux G, Thirion B.
PMID: 29497357
Front Neurosci. 2018 Feb 14;12:64. doi: 10.3389/fnins.2018.00064. eCollection 2018.

In Echo-Planar Imaging (EPI)-based Magnetic Resonance Imaging (MRI), inter-subject registration typically uses the subject's T1-weighted (T1w) anatomical image to learn deformations of the subject's brain onto a template. The estimated deformation fields are then applied to the subject's EPI...

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Dohmatob E, Varoquaux G, Thirion B. Inter-subject Registration of Functional Images: Do We Need Anatomical Images?. Front Neurosci. 2018;12:64doi: 10.3389/fnins.2018.00064.
Dohmatob, E., Varoquaux, G., & Thirion, B. (2018). Inter-subject Registration of Functional Images: Do We Need Anatomical Images?. Frontiers in neuroscience, 1264. https://doi.org/10.3389/fnins.2018.00064
Dohmatob, Elvis, et al. "Inter-subject Registration of Functional Images: Do We Need Anatomical Images?." Frontiers in neuroscience vol. 12 (2018): 64. doi: https://doi.org/10.3389/fnins.2018.00064
Dohmatob E, Varoquaux G, Thirion B. Inter-subject Registration of Functional Images: Do We Need Anatomical Images?. Front Neurosci. 2018 Feb 14;12:64. doi: 10.3389/fnins.2018.00064. eCollection 2018. PMID: 29497357; PMCID: PMC5819565.
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Unfolding the Genome: The Case Study of P. falciparum.

The international journal of biostatistics

Varoquaux N.
PMID: 29878883
Int J Biostat. 2018 Jun 07;15(2). doi: 10.1515/ijb-2017-0061.

The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome architecture. 3C-like methods coupled with high-throughput sequencing can now assess physical interactions...

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Varoquaux N. Unfolding the Genome: The Case Study of P. falciparum. Int J Biostat. 2018;15(2)doi: 10.1515/ijb-2017-0061.
Varoquaux, N. (2018). Unfolding the Genome: The Case Study of P. falciparum. The international journal of biostatistics, 15(2), . https://doi.org/10.1515/ijb-2017-0061
Varoquaux, Nelle. "Unfolding the Genome: The Case Study of P. falciparum." The international journal of biostatistics vol. 15,2 (2018). doi: https://doi.org/10.1515/ijb-2017-0061
Varoquaux N. Unfolding the Genome: The Case Study of P. falciparum. Int J Biostat. 2018 Jun 07;15(2). doi: 10.1515/ijb-2017-0061. PMID: 29878883.
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Prediction, Not Association, Paves the Road to Precision Medicine.

JAMA psychiatry

Bzdok D, Varoquaux G, Steyerberg EW.
PMID: 32804995
JAMA Psychiatry. 2021 Feb 01;78(2):127-128. doi: 10.1001/jamapsychiatry.2020.2549.

No abstract available.

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Bzdok D, Varoquaux G, Steyerberg EW. Prediction, Not Association, Paves the Road to Precision Medicine. JAMA Psychiatry. 2021;78(2):127-128doi: 10.1001/jamapsychiatry.2020.2549.
Bzdok, D., Varoquaux, G., & Steyerberg, E. W. (2021). Prediction, Not Association, Paves the Road to Precision Medicine. JAMA psychiatry, 78(2), 127-128. https://doi.org/10.1001/jamapsychiatry.2020.2549
Bzdok, Danilo, et al. "Prediction, Not Association, Paves the Road to Precision Medicine." JAMA psychiatry vol. 78,2 (2021): 127-128. doi: https://doi.org/10.1001/jamapsychiatry.2020.2549
Bzdok D, Varoquaux G, Steyerberg EW. Prediction, Not Association, Paves the Road to Precision Medicine. JAMA Psychiatry. 2021 Feb 01;78(2):127-128. doi: 10.1001/jamapsychiatry.2020.2549. PMID: 32804995.
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Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks.

PloS one

Kiar G, Chatelain Y, de Oliveira Castro P, Petit E, Rokem A, Varoquaux G, Misic B, Evans AC, Glatard T.
PMID: 34724000
PLoS One. 2021 Nov 01;16(11):e0250755. doi: 10.1371/journal.pone.0250755. eCollection 2021.

The analysis of brain-imaging data requires complex processing pipelines to support findings on brain function or pathologies. Recent work has shown that variability in analytical decisions, small amounts of noise, or computational environments can lead to substantial differences in...

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Kiar G, Chatelain Y, de Oliveira Castro P, et al. Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks. PLoS One. 2021;16(11):e0250755doi: 10.1371/journal.pone.0250755.
Kiar, G., Chatelain, Y., de Oliveira Castro, P., Petit, E., Rokem, A., Varoquaux, G., Misic, B., Evans, A. C., & Glatard, T. (2021). Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks. PloS one, 16(11), e0250755. https://doi.org/10.1371/journal.pone.0250755
Kiar, Gregory, et al. "Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks." PloS one vol. 16,11 (2021): e0250755. doi: https://doi.org/10.1371/journal.pone.0250755
Kiar G, Chatelain Y, de Oliveira Castro P, Petit E, Rokem A, Varoquaux G, Misic B, Evans AC, Glatard T. Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks. PLoS One. 2021 Nov 01;16(11):e0250755. doi: 10.1371/journal.pone.0250755. eCollection 2021. PMID: 34724000; PMCID: PMC8559953.
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Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium .

Plants (Basel, Switzerland)

Kechid M, Desbrosses G, Gamet L, Castaings L, Varoquaux F, Djekoun A, Touraine B.
PMID: 35009131
Plants (Basel). 2022 Jan 04;11(1). doi: 10.3390/plants11010128.

No abstract available.

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Kechid M, Desbrosses G, Gamet L, et al. Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium . Plants (Basel). 2022;11(1)doi: 10.3390/plants11010128.
Kechid, M., Desbrosses, G., Gamet, L., Castaings, L., Varoquaux, F., Djekoun, A., & Touraine, B. (2022). Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium . Plants (Basel, Switzerland), 11(1), . https://doi.org/10.3390/plants11010128
Kechid, Maya, et al. "Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium ." Plants (Basel, Switzerland) vol. 11,1 (2022). doi: https://doi.org/10.3390/plants11010128
Kechid M, Desbrosses G, Gamet L, Castaings L, Varoquaux F, Djekoun A, Touraine B. Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium . Plants (Basel). 2022 Jan 04;11(1). doi: 10.3390/plants11010128. PMID: 35009131.
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Subject-specific segregation of functional territories based on deep phenotyping.

Human brain mapping

Pinho AL, Amadon A, Fabre M, Dohmatob E, Denghien I, Torre JJ, Ginisty C, Becuwe-Desmidt S, Roger S, Laurier L, Joly-Testault V, Médiouni-Cloarec G, Doublé C, Martins B, Pinel P, Eger E, Varoquaux G, Pallier C, Dehaene S, Hertz-Pannier L, Thirion B.
PMID: 33368868
Hum Brain Mapp. 2021 Mar;42(4):841-870. doi: 10.1002/hbm.25189. Epub 2020 Dec 24.

Functional magnetic resonance imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed...

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Pinho AL, Amadon A, Fabre M, et al. Subject-specific segregation of functional territories based on deep phenotyping. Hum Brain Mapp. 2020;42(4):841-870doi: 10.1002/hbm.25189.
Pinho, A. L., Amadon, A., Fabre, M., Dohmatob, E., Denghien, I., Torre, J. J., Ginisty, C., Becuwe-Desmidt, S., Roger, S., Laurier, L., Joly-Testault, V., Médiouni-Cloarec, G., Doublé, C., Martins, B., Pinel, P., Eger, E., Varoquaux, G., Pallier, C., Dehaene, S., Hertz-Pannier, L., & Thirion, B. (2021). Subject-specific segregation of functional territories based on deep phenotyping. Human brain mapping, 42(4), 841-870. https://doi.org/10.1002/hbm.25189
Pinho, Ana Luísa, et al. "Subject-specific segregation of functional territories based on deep phenotyping." Human brain mapping vol. 42,4 (2021): 841-870. doi: https://doi.org/10.1002/hbm.25189
Pinho AL, Amadon A, Fabre M, Dohmatob E, Denghien I, Torre JJ, Ginisty C, Becuwe-Desmidt S, Roger S, Laurier L, Joly-Testault V, Médiouni-Cloarec G, Doublé C, Martins B, Pinel P, Eger E, Varoquaux G, Pallier C, Dehaene S, Hertz-Pannier L, Thirion B. Subject-specific segregation of functional territories based on deep phenotyping. Hum Brain Mapp. 2021 Mar;42(4):841-870. doi: 10.1002/hbm.25189. Epub 2020 Dec 24. PMID: 33368868; PMCID: PMC7856658.
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Correction: Comparative genomics and the nature of placozoan species.

PLoS biology

Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G.
PMID: 30231017
PLoS Biol. 2018 Sep 19;16(9):e3000032. doi: 10.1371/journal.pbio.3000032. eCollection 2018 Sep.

[This corrects the article DOI: 10.1371/journal.pbio.2005359.].

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Eitel M, Francis WR, Varoqueaux F, et al. Correction: Comparative genomics and the nature of placozoan species. PLoS Biol. 2018;16(9):e3000032doi: 10.1371/journal.pbio.3000032.
Eitel, M., Francis, W. R., Varoqueaux, F., Daraspe, J., Osigus, H. J., Krebs, S., Vargas, S., Blum, H., Williams, G. A., Schierwater, B., & Wörheide, G. (2018). Correction: Comparative genomics and the nature of placozoan species. PLoS biology, 16(9), e3000032. https://doi.org/10.1371/journal.pbio.3000032
Eitel, Michael, et al. "Correction: Comparative genomics and the nature of placozoan species." PLoS biology vol. 16,9 (2018): e3000032. doi: https://doi.org/10.1371/journal.pbio.3000032
Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Correction: Comparative genomics and the nature of placozoan species. PLoS Biol. 2018 Sep 19;16(9):e3000032. doi: 10.1371/journal.pbio.3000032. eCollection 2018 Sep. PMID: 30231017; PMCID: PMC6145499.
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Showing 1 to 12 of 60 entries