Ciftify: A framework for surface-based analysis of legacy MR acquisitions.
Journal
NeuroImage
ISSN: 1095-9572
Titre abrégé: Neuroimage
Pays: United States
ID NLM: 9215515
Informations de publication
Date de publication:
15 08 2019
15 08 2019
Historique:
received:
28
02
2019
revised:
26
04
2019
accepted:
29
04
2019
pubmed:
16
5
2019
medline:
25
1
2020
entrez:
16
5
2019
Statut:
ppublish
Résumé
The preprocessing pipelines of the Human Connectome Project (HCP) were made publicly available for the neuroimaging community to apply the HCP analytic approach to data from non-HCP sources. The HCP analytic approach is surface-based for the cerebral cortex, uses the CIFTI "grayordinate" file format, provides greater statistical sensitivity than traditional volume-based analysis approaches, and allows for a more neuroanatomically-faithful representation of data. However, the HCP pipelines require the acquisition of specific images (namely T2w and field map) that historically have often not been acquired. Massive amounts of this 'legacy' data could benefit from the adoption of HCP-style methods. However, there is currently no published framework, to our knowledge, for adapting HCP preprocessing to "legacy" data. Here we present the ciftify project, a parsimonious analytic framework for adapting key modules from the HCP pipeline into existing structural workflows using FreeSurfer's recon_all structural and existing functional preprocessing workflows. Within this framework, any functional dataset with an accompanying (i.e. T1w) anatomical data can be analyzed in CIFTI format. To simplify usage for new data, the workflow has been bundled with fMRIPrep following the BIDS-app framework. Finally, we present the package and comment on future neuroinformatics advances that may accelerate the movement to a CIFTI-based grayordinate framework.
Identifiants
pubmed: 31091476
pii: S1053-8119(19)30371-4
doi: 10.1016/j.neuroimage.2019.04.078
pmc: PMC6675413
mid: NIHMS1530980
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
818-826Subventions
Organisme : NIMH NIH HHS
ID : F30 MH097312
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH060974
Pays : United States
Organisme : NIMH NIH HHS
ID : R24 MH108315
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Informations de copyright
Copyright © 2019 Elsevier Inc. All rights reserved.
Références
IEEE Trans Med Imaging. 2002 Oct;21(10):1280-91
pubmed: 12585710
Front Neuroinform. 2013 Jul 08;7:12
pubmed: 23847528
Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6356-E6365
pubmed: 29925602
Nat Neurosci. 2016 Nov;19(11):1523-1536
pubmed: 27643430
Neuroimage. 2017 Jan;144(Pt B):270-274
pubmed: 27074495
Nat Methods. 2019 Jan;16(1):111-116
pubmed: 30532080
Neuron. 2017 Jul 19;95(2):457-471.e5
pubmed: 28728026
PLoS Comput Biol. 2017 Mar 9;13(3):e1005209
pubmed: 28278228
Sci Data. 2016 Dec 06;3:160102
pubmed: 27922621
Nat Commun. 2018 Jul 19;9(1):2818
pubmed: 30026557
Neuroimage. 2012 Oct 1;62(4):2222-31
pubmed: 22366334
Neuron. 2018 Aug 22;99(4):640-663
pubmed: 30138588
Nat Neurosci. 2015 Dec;18(12):1853-60
pubmed: 26551545
PLoS One. 2016 Mar 30;11(3):e0152472
pubmed: 27027775
Neuroimage. 2014 Jun;93 Pt 2:165-75
pubmed: 23567887
Front Neuroinform. 2014 Feb 21;8:14
pubmed: 24600388
Neuroimage. 2018 Nov 1;181:692-717
pubmed: 29753843
Neuroimage. 2014 May 15;92:381-97
pubmed: 24530839
Front Neuroinform. 2015 Apr 10;9:8
pubmed: 25914639
Hum Brain Mapp. 2006 Jan;27(1):14-27
pubmed: 16035046
J Neurosci. 2011 Aug 10;31(32):11597-616
pubmed: 21832190
Neuron. 2013 Feb 6;77(3):586-95
pubmed: 23395382
Neuroimage. 2013 Oct 15;80:202-19
pubmed: 23707591
Neuroimage. 2015 Dec;123:253-68
pubmed: 26074200
Neuroimage. 2013 Oct 15;80:105-24
pubmed: 23668970
Neuroimage. 2013 Nov 1;81:400-411
pubmed: 23685161
Neuroimage. 2013 Oct 15;80:62-79
pubmed: 23684880
Neuroimage. 2003 Oct;20(2):870-88
pubmed: 14568458
Front Hum Neurosci. 2014 May 16;8:239
pubmed: 24904347
Neuroimage. 2008 Jul 1;41(3):835-48
pubmed: 18434199
Nature. 2012 Apr 04;484(7392):24-6
pubmed: 22481337
Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12574-12579
pubmed: 27791099
Cereb Cortex. 2018 Sep 1;28(9):3095-3114
pubmed: 28981612
Sci Data. 2016 Jun 21;3:160044
pubmed: 27326542
Neuroimage. 2006 Jul 1;31(3):968-80
pubmed: 16530430
Neuroimage. 2012 Nov 15;63(3):1443-53
pubmed: 22732555
Neuroimage. 2005 Nov 15;28(3):635-62
pubmed: 16172003
Neuroimage. 2016 Jan 1;124(Pt B):1065-1068
pubmed: 26574120
Hum Brain Mapp. 2006 May;27(5):392-401
pubmed: 16596654
Neuroimage. 2012 Aug 15;62(2):757-64
pubmed: 22062192
Nat Neurosci. 2014 Nov;17(11):1510-7
pubmed: 25349916
Neuroimage. 2002 May;16(1):217-40
pubmed: 11969330
Neuroimage. 2018 Feb 15;167:453-465
pubmed: 29100940
Neuroimage. 2014 Oct 15;100:414-26
pubmed: 24939340
Cereb Cortex. 2019 Jun 1;29(6):2533-2551
pubmed: 29878084
Neuroimage. 2009 Oct 15;48(1):63-72
pubmed: 19573611
Curr Treat Options Psychiatry. 2017 Jun;4(2):196-209
pubmed: 29038777
Neuroimage. 2007 Jan 15;34(2):550-64
pubmed: 17110131
Neuroimage. 2014 Apr 15;90:449-68
pubmed: 24389422
Neuroimage. 2013 Oct 15;80:80-104
pubmed: 23702417
Nature. 2016 Aug 11;536(7615):171-178
pubmed: 27437579
J Neurophysiol. 2011 Sep;106(3):1125-65
pubmed: 21653723
Neuroimage. 1999 Feb;9(2):195-207
pubmed: 9931269
Neuroimage. 2012 Aug 15;62(2):774-81
pubmed: 22248573
Nat Methods. 2011 Jun 26;8(8):665-70
pubmed: 21706013
Neuroimage. 2017 Sep;158:346-355
pubmed: 28716714
Front Neuroinform. 2017 Feb 21;11:17
pubmed: 28270762
Nat Neurosci. 2016 Aug 26;19(9):1175-87
pubmed: 27571196