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Volumn 13, Issue 3, 2017, Pages

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

(29)  Gorgolewski, Krzysztof J a   Alfaro Almagro, Fidel b   Auer, Tibor c   Bellec, Pierre d,e   Capotă, Mihai f,aa   Chakravarty, M Mallar g,h   Churchill, Nathan W i   Cohen, Alexander Li j   Craddock, R Cameron k,l   Devenyi, Gabriel A g,h   Eklund, Anders m   Esteban, Oscar a   Flandin, Guillaume n   Ghosh, Satrajit S o,p   Guntupalli, J Swaroop q   Jenkinson, Mark b   Keshavan, Anisha r   Kiar, Gregory s,t   Liem, Franziskus u   Raamana, Pradeep Reddy v,w   more..


Author keywords

[No Author keywords available]

Indexed keywords

BRAIN MAPPING; DATA HANDLING;

EID: 85016747642     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005209     Document Type: Article
Times cited : (215)

References (52)
  • 2
    • 84863918721 scopus 로고    scopus 로고
    • Open is not enough. Let’ s take the next step: An integrated, community-driven computing platform for neuroscience
    • Halchenko YO, Hanke M, Open is not enough. Let’ s take the next step: An integrated, community-driven computing platform for neuroscience. Front Neuroinform. 2012;6.
    • (2012) Front Neuroinform , vol.6
    • Halchenko, Y.O.1    Hanke, M.2
  • 3
    • 84936764209 scopus 로고    scopus 로고
    • A purely confirmatory replication study of structural brain-behavior correlations
    • 568444
    • Boekel W, Wagenmakers E-J, Belay L, Verhagen J, Brown S, Forstmann BU, A purely confirmatory replication study of structural brain-behavior correlations. Cortex. 2015;66: 115–133. doi: 10.1016/j.cortex.2014.11.01925684445
    • (2015) Cortex , vol.66 , pp. 115-133
    • Boekel, W.1    Wagenmakers, E.-J.2    Belay, L.3    Verhagen, J.4    Brown, S.5    Forstmann, B.U.6
  • 5
    • 84861728837 scopus 로고    scopus 로고
    • The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements
    • 267552
    • Gronenschild EHBM, Habets P, Jacobs HIL, Mengelers R, Rozendaal N, van Os J, Hayasaka S, et al. The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements. PLoS One. 2012;7: e38234. doi: 10.1371/journal.pone.003823422675527
    • (2012) PLoS One , vol.7 , pp. 38234
    • Gronenschild, E.H.B.M.1    Habets, P.2    Jacobs, H.I.L.3    Mengelers, R.4    Rozendaal, N.5    van Os, J.6    Hayasaka, S.7
  • 7
    • 80052121849 scopus 로고    scopus 로고
    • CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing
    • 187810
    • Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011;12: 356. doi: 10.1186/1471-2105-12-35621878105
    • (2011) BMC Bioinformatics , vol.12 , pp. 356
    • Angiuoli, S.V.1    Matalka, M.2    Gussman, A.3    Galens, K.4    Vangala, M.5    Riley, D.R.6
  • 8
    • 84858330364 scopus 로고    scopus 로고
    • Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
    • 242953
    • Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, et al. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics. 2012;13: 42. doi: 10.1186/1471-2105-13-4222429538
    • (2012) BMC Bioinformatics , vol.13 , pp. 42
    • Krampis, K.1    Booth, T.2    Chapman, B.3    Tiwari, B.4    Bicak, M.5    Field, D.6
  • 9
    • 84973886308 scopus 로고    scopus 로고
    • NGSeasy: a next generation sequencing pipeline in Docker containers
    • Folarin AA, Dobson RJB, Newhouse SJ, NGSeasy: a next generation sequencing pipeline in Docker containers. F1000Res. 2015;4.
    • (2015) F1000Res , vol.4
    • Folarin, A.A.1    Dobson, R.J.B.2    Newhouse, S.J.3
  • 10
    • 84970983912 scopus 로고    scopus 로고
    • BioShaDock: a community driven bioinformatics shared Docker-based tools registry
    • 691319
    • Moreews F, Sallou O, Ménager H, Le Bras Y, Monjeaud C, Blanchet C, et al. BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Res. 2015;4: 1443. doi: 10.12688/f1000research.7536.126913191
    • (2015) F1000Res , vol.4 , pp. 1443
    • Moreews, F.1    Sallou, O.2    Ménager, H.3    Le Bras, Y.4    Monjeaud, C.5    Blanchet, C.6
  • 12
    • 84979503019 scopus 로고    scopus 로고
    • Bioboxes: standardised containers for interchangeable bioinformatics software
    • 647302
    • Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD, Bioboxes: standardised containers for interchangeable bioinformatics software. Gigascience. 2015;4: 47. doi: 10.1186/s13742-015-0087-026473029
    • (2015) Gigascience , vol.4 , pp. 47
    • Belmann, P.1    Dröge, J.2    Bremges, A.3    McHardy, A.C.4    Sczyrba, A.5    Barton, M.D.6
  • 13
    • 84858593012 scopus 로고    scopus 로고
    • The iPlant collaborative: cyberinfrastructure for plant biology
    • Available
    • Jordan C, Skidmore E, Dooley R, The iPlant collaborative: cyberinfrastructure for plant biology. Front Plant Sci. journal.frontiersin.org; 2011; Available: http://journal.frontiersin.org/article/10.3389/fpls.2011.00034/full
    • (2011) Front Plant Sci. journal.frontiersin.org
    • Jordan, C.1    Skidmore, E.2    Dooley, R.3
  • 14
    • 85016713405 scopus 로고    scopus 로고
    • urtzer GM. Singularity 2.1.2—Linux application and environment containers for science [Internet]. 2016
    • Kurtzer GM. Singularity 2.1.2—Linux application and environment containers for science [Internet]. 2016.
  • 15
    • 84975789666 scopus 로고    scopus 로고
    • The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments
    • 732654
    • Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, et al. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data. 2016;3: 160044. doi: 10.1038/sdata.2016.4427326542
    • (2016) Sci Data , vol.3 , pp. 160044
    • Gorgolewski, K.J.1    Auer, T.2    Calhoun, V.D.3    Craddock, R.C.4    Das, S.5    Duff, E.P.6
  • 16
    • 84994026358 scopus 로고    scopus 로고
    • Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python
    • 189781
    • Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, et al. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python. Front Neuroinform. 2011;5: 13. doi: 10.3389/fninf.2011.0001321897815
    • (2011) Front Neuroinform , vol.5 , pp. 13
    • Gorgolewski, K.1    Burns, C.D.2    Madison, C.3    Clark, D.4    Halchenko, Y.O.5    Waskom, M.L.6
  • 17
    • 37549003336 scopus 로고    scopus 로고
    • MapReduce: simplified data processing on large clusters
    • Dean J, Ghemawat S, MapReduce: simplified data processing on large clusters. Commun ACM. 2008;51: 107.
    • (2008) Commun ACM , vol.51 , pp. 107
    • Dean, J.1    Ghemawat, S.2
  • 19
    • 84862997809 scopus 로고    scopus 로고
    • FreeSurfer
    • 224857
    • Fischl B, FreeSurfer. Neuroimage. 2012;62: 774–781. doi: 10.1016/j.neuroimage.2012.01.02122248573
    • (2012) Neuroimage , vol.62 , pp. 774-781
    • Fischl, B.1
  • 20
    • 84861414424 scopus 로고    scopus 로고
    • Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis
    • 243049
    • Reuter M, Schmansky NJ, Rosas HD, Fischl B, Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis. Neuroimage. 2012;61: 1402–1418. doi: 10.1016/j.neuroimage.2012.02.08422430496
    • (2012) Neuroimage , vol.61 , pp. 1402-1418
    • Reuter, M.1    Schmansky, N.J.2    Rosas, H.D.3    Fischl, B.4
  • 23
    • 84896984583 scopus 로고    scopus 로고
    • BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs
    • 467247
    • Eklund A, Dufort P, Villani M, Laconte S, BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs. Front Neuroinform. 2014;8: 24. doi: 10.3389/fninf.2014.0002424672471
    • (2014) Front Neuroinform , vol.8 , pp. 24
    • Eklund, A.1    Dufort, P.2    Villani, M.3    Laconte, S.4
  • 24
    • 84930652853 scopus 로고    scopus 로고
    • Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres
    • 600450
    • Raffelt DA, Smith RE, Ridgway GR, Tournier J-D, Vaughan DN, Rose S, et al. Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres. Neuroimage. 2015;117: 40–55. doi: 10.1016/j.neuroimage.2015.05.03926004503
    • (2015) Neuroimage , vol.117 , pp. 40-55
    • Raffelt, D.A.1    Smith, R.E.2    Ridgway, G.R.3    Tournier, J.-D.4    Vaughan, D.N.5    Rose, S.6
  • 27
    • 85015404202 scopus 로고    scopus 로고
    • The Preprocessed Connectomes Project Quality Assessment Protocol—a resource for measuring the quality of MRI data
    • Zarrar S, Steven G, Qingyang L, Yassine B, Chaogan Y, Zhen Y, et al. The Preprocessed Connectomes Project Quality Assessment Protocol—a resource for measuring the quality of MRI data. Front Neurosci. 2015;9.
    • (2015) Front Neurosci , vol.9
    • Zarrar, S.1    Steven, G.2    Qingyang, L.3    Yassine, B.4    Chaogan, Y.5    Zhen, Y.6
  • 28
    • 84991528997 scopus 로고    scopus 로고
    • Towards Automated Analysis of Connectomes: The Configurable Pipeline for the Analysis of Connectomes (C-PAC)
    • Craddock C, Sikka S, Cheung B, Khanuja R, Ghosh SS, Yan C, et al. Towards Automated Analysis of Connectomes: The Configurable Pipeline for the Analysis of Connectomes (C-PAC). Front Neuroinform.
    • Front Neuroinform
    • Craddock, C.1    Sikka, S.2    Cheung, B.3    Khanuja, R.4    Ghosh, S.S.5    Yan, C.6
  • 30
    • 84870906999 scopus 로고    scopus 로고
    • 101 labeled brain images and a consistent human cortical labeling protocol
    • 322700
    • Klein A, Tourville J, 101 labeled brain images and a consistent human cortical labeling protocol. Front Neurosci. 2012;6: 171. doi: 10.3389/fnins.2012.0017123227001
    • (2012) Front Neurosci , vol.6 , pp. 171
    • Klein, A.1    Tourville, J.2
  • 31
    • 84910045464 scopus 로고    scopus 로고
    • The effects of SIFT on the reproducibility and biological accuracy of the structural connectome
    • 531277
    • Smith RE, Tournier J-D, Calamante F, Connelly A, The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. Neuroimage. 2015;104: 253–265. doi: 10.1016/j.neuroimage.2014.10.00425312774
    • (2015) Neuroimage , vol.104 , pp. 253-265
    • Smith, R.E.1    Tournier, J.-D.2    Calamante, F.3    Connelly, A.4
  • 33
    • 84920997437 scopus 로고    scopus 로고
    • Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML
    • 564218
    • Cusack R, Vicente-Grabovetsky A, Mitchell DJ, Wild CJ, Auer T, Linke AC, et al. Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML. Front Neuroinform. 2014;8: 90. doi: 10.3389/fninf.2014.0009025642185
    • (2014) Front Neuroinform , vol.8 , pp. 90
    • Cusack, R.1    Vicente-Grabovetsky, A.2    Mitchell, D.J.3    Wild, C.J.4    Auer, T.5    Linke, A.C.6
  • 34
    • 84858060836 scopus 로고    scopus 로고
    • The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows
    • 249357
    • Bellec P, Lavoie-Courchesne S, Dickinson P, Lerch JP, Zijdenbos AP, Evans AC, The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front Neuroinform. 2012;6: 7. doi: 10.3389/fninf.2012.0000722493575
    • (2012) Front Neuroinform , vol.6 , pp. 7
    • Bellec, P.1    Lavoie-Courchesne, S.2    Dickinson, P.3    Lerch, J.P.4    Zijdenbos, A.P.5    Evans, A.C.6
  • 38
    • 0036338502 scopus 로고    scopus 로고
    • The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis framework
    • 190621
    • Strother SC, Anderson J, Hansen LK, Kjems U, Kustra R, Sidtis J, et al. The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis framework. Neuroimage. 2002;15: 747–771. doi: 10.1006/nimg.2001.103411906218
    • (2002) Neuroimage , vol.15 , pp. 747-771
    • Strother, S.C.1    Anderson, J.2    Hansen, L.K.3    Kjems, U.4    Kustra, R.5    Sidtis, J.6
  • 39
    • 84856746200 scopus 로고    scopus 로고
    • Optimizing preprocessing and analysis pipelines for single-subject fMRI. I. Standard temporal motion and physiological noise correction methods
    • 145594
    • Churchill NW, Oder A, Abdi H, Tam F, Lee W, Thomas C, et al. Optimizing preprocessing and analysis pipelines for single-subject fMRI. I. Standard temporal motion and physiological noise correction methods. Hum Brain Mapp. 2012;33: 609–627. doi: 10.1002/hbm.2123821455942
    • (2012) Hum Brain Mapp , vol.33 , pp. 609-627
    • Churchill, N.W.1    Oder, A.2    Abdi, H.3    Tam, F.4    Lee, W.5    Thomas, C.6
  • 40
    • 84857569633 scopus 로고    scopus 로고
    • Optimizing preprocessing and analysis pipelines for single-subject fMRI: 2. Interactions with ICA, PCA, task contrast and inter-subject heterogeneity
    • 238399
    • Churchill NW, Yourganov G, Oder A, Tam F, Graham SJ, Strother SC, Optimizing preprocessing and analysis pipelines for single-subject fMRI: 2. Interactions with ICA, PCA, task contrast and inter-subject heterogeneity. PLoS One. 2012;7: e31147. doi: 10.1371/journal.pone.003114722383999
    • (2012) PLoS One , vol.7 , pp. 31147
    • Churchill, N.W.1    Yourganov, G.2    Oder, A.3    Tam, F.4    Graham, S.J.5    Strother, S.C.6
  • 41
    • 84941336224 scopus 로고    scopus 로고
    • An Automated, Adaptive Framework for Optimizing Preprocessing Pipelines in Task-Based Functional MRI
    • 616166
    • Churchill NW, Spring R, Afshin-Pour B, Dong F, Strother SC, An Automated, Adaptive Framework for Optimizing Preprocessing Pipelines in Task-Based Functional MRI. PLoS One. 2015;10: e0131520. doi: 10.1371/journal.pone.013152026161667
    • (2015) PLoS One , vol.10 , pp. 131520
    • Churchill, N.W.1    Spring, R.2    Afshin-Pour, B.3    Dong, F.4    Strother, S.C.5
  • 42
    • 84925273002 scopus 로고    scopus 로고
    • Striatal shape abnormalities as novel neurodevelopmental endophenotypes in schizophrenia: a longitudinal study
    • 550493
    • Chakravarty MM, Rapoport JL, Giedd JN, Raznahan A, Shaw P, Collins DL, et al. Striatal shape abnormalities as novel neurodevelopmental endophenotypes in schizophrenia: a longitudinal study. Hum Brain Mapp. 2015;36: 1458–1469. doi: 10.1002/hbm.2271525504933
    • (2015) Hum Brain Mapp , vol.36 , pp. 1458-1469
    • Chakravarty, M.M.1    Rapoport, J.L.2    Giedd, J.N.3    Raznahan, A.4    Shaw, P.5    Collins, D.L.6
  • 43
    • 84907028232 scopus 로고    scopus 로고
    • Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates
    • 478480
    • Pipitone J, Park MTM, Winterburn J, Lett TA, Lerch JP, Pruessner JC, et al. Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates. Neuroimage. 2014;101: 494–512. doi: 10.1016/j.neuroimage.2014.04.05424784800
    • (2014) Neuroimage , vol.101 , pp. 494-512
    • Pipitone, J.1    Park, M.T.M.2    Winterburn, J.3    Lett, T.A.4    Lerch, J.P.5    Pruessner, J.C.6
  • 44
    • 84898644619 scopus 로고    scopus 로고
    • Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation using multiple automatically generated templates
    • 465735
    • Park MTM, Pipitone J, Baer LH, Winterburn JL, Shah Y, Chavez S, et al. Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation using multiple automatically generated templates. Neuroimage. 2014;95: 217–231. doi: 10.1016/j.neuroimage.2014.03.03724657354
    • (2014) Neuroimage , vol.95 , pp. 217-231
    • Park, M.T.M.1    Pipitone, J.2    Baer, L.H.3    Winterburn, J.L.4    Shah, Y.5    Chavez, S.6
  • 45
    • 84883746714 scopus 로고    scopus 로고
    • Performing label-fusion-based segmentation using multiple automatically generated templates
    • 261103
    • Chakravarty MM, Steadman P, van Eede MC, Calcott RD, Gu V, Shaw P, et al. Performing label-fusion-based segmentation using multiple automatically generated templates. Hum Brain Mapp. 2013;34: 2635–2654. doi: 10.1002/hbm.2209222611030
    • (2013) Hum Brain Mapp , vol.34 , pp. 2635-2654
    • Chakravarty, M.M.1    Steadman, P.2    van Eede, M.C.3    Calcott, R.D.4    Gu, V.5    Shaw, P.6
  • 46
    • 84994044903 scopus 로고    scopus 로고
    • Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy
    • 201673
    • Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, et al. Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Front Neuroinform. 2011;5: 23. doi: 10.3389/fninf.2011.0002322016733
    • (2011) Front Neuroinform , vol.5 , pp. 23
    • Yendiki, A.1    Panneck, P.2    Srinivasan, P.3    Stevens, A.4    Zöllei, L.5    Augustinack, J.6
  • 47
    • 84944903287 scopus 로고    scopus 로고
    • The impact of Docker containers on the performance of genomic pipelines
    • 642124
    • Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C, The impact of Docker containers on the performance of genomic pipelines. PeerJ. 2015;3: e1273. doi: 10.7717/peerj.127326421241
    • (2015) PeerJ , vol.3 , pp. 1273
    • Di Tommaso, P.1    Palumbo, E.2    Chatzou, M.3    Prieto, P.4    Heuer, M.L.5    Notredame, C.6
  • 49
    • 84901447087 scopus 로고    scopus 로고
    • CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research
    • 490440
    • Sherif T, Rioux P, Rousseau M-E, Kassis N, Beck N, Adalat R, et al. CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. Front Neuroinform. 2014;8: 54. doi: 10.3389/fninf.2014.0005424904400
    • (2014) Front Neuroinform , vol.8 , pp. 54
    • Sherif, T.1    Rioux, P.2    Rousseau, M.-E.3    Kassis, N.4    Beck, N.5    Adalat, R.6
  • 51
    • 85016805278 scopus 로고    scopus 로고
    • Containers for portable, productive and performant scientific computing
    • Internet
    • Hale JS, Li L, Richardson CN, Wells GN, Containers for portable, productive and performant scientific computing [Internet]. arXiv [cs.DC]. 2016. http://arxiv.org/abs/1608.07573
    • (2016) arXiv [cs.DC]
    • Hale, J.S.1    Li, L.2    Richardson, C.N.3    Wells, G.N.4
  • 52
    • 85016734933 scopus 로고    scopus 로고
    • MRIQC: Predicting Quality in Manual MRI Assessment Protocols Using No-Reference Image Quality Measures
    • ebruary, Retrieved February 27, 2017, fro
    • Esteban O., Birman D., Schaer M., Koyejo O. O., Poldrack R. A., Gorgolewski K. J., (2017, February24). MRIQC: Predicting Quality in Manual MRI Assessment Protocols Using No-Reference Image Quality Measures. bioRxiv. Retrieved February 27, 2017, from http://biorxiv.org/content/early/2017/02/24/111294
    • (2017) bioRxiv
    • Esteban, O.1    Birman, D.2    Schaer, M.3    Koyejo, O.O.4    Poldrack, R.A.5    Gorgolewski, K.J.6


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