BRAPH

グラフ理論解析のグラフィカルツールボックス。
名前がセンスある。

論文
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178798
ダウンロード
http://braph.org/software/
指標の説明が非常によい
http://braph.org/manual/graph-measures/

Dynamic graph metrics

Neuroimage. 2017 Jul 11. pii: S1053-8119(17)30584-0. doi: 10.1016/j.neuroimage.2017.07.016. [Epub ahead of print]
Evaluating the replicability, specificity, and generalizability of connectome fingerprints.
Waller L1, Walter H1, Kruschwitz JD1, Reuter L1, Müller S1, Erk S1, Veer IM2.

前いじったときはいまいちだった。
けど、DCCと組み合わせらいいかもん。

動的機能結合はDCC

Comparing test-retest reliability of dynamic functional connectivity methods.
Neuroimage. 2017 Jul 04;:
Authors: Choe AS, Nebel MB, Barber AD, Cohen JR, Xu Y, Pekar JJ, Caffo B, Lindquist MA

dynamic conditional correlations (DCC) methodsがよさそうとのこと。

Modelling and Interpreting Mesoscale Network Dynamics

Modelling and Interpreting Mesoscale Network Dynamics.
Neuroimage. 2017 Jun 20;:
Authors: Khambhati AN, Sizemore AE, Betzel RF, Bassett DS

Bassettさんとこから。
つんどくん。

Theta band transcranial alternating current stimulations modulates network behavior of dorsal anterior cingulate cortex.

Sci Rep. 2017 Jun 15;7(1):3607. doi: 10.1038/s41598-017-03859-7.Theta band transcranial alternating current stimulations modulates network behavior of dorsal anterior cingulate cortex. Onoda K, Kawagoe T, Zheng H Yamaguchi S.

いろいろとあーーーーorzとなったけどとりあえず出た。

機能的結合のビッグデータ

Functional connectomics from a "big data" perspective.
Neuroimage. 2017 Feb 14;:
Authors: Xia M, He Y

こっちはrsfMRIのみ。
1000 Functional Connectomes Project http://fcon_1000.projects.nitrc.org/fcpClassic/FcpTable.html
Human Connectome Project http://www.humanconnectome.org/
Consortium for Reliability and Reproducibility http://fcon_1000.projects.nitrc.org/indi/CoRR/html/index.html
Enhancing Neuro Imaging Genetics through Meta Analysis http://enigma.ini.usc.edu/
Alzheimer's Disease Neuroimaging Initiative http://adni.loni.usc.edu/
Attention Deficit Hyperactivity Disorder 200 http://fcon_1000.projects.nitrc.org/indi/adhd200/
National Database for Autism Research https://ndar.nih.gov/
UK BioBank https://www.ukbiobank.ac.uk/
MyConnectome Project http://myconnectome.org/wp/
OpenfMRI https://openfmri.org/

脳画像生体バンク

Improving data availability for brain image biobanking in healthy subjects: practice-based suggestions from an international multidisciplinary working group.
Neuroimage. 2017 Feb 13;:
Authors: BRAINS (Brain Imaging in Normal Subjects) Expert Working Group, Shenkin SD, Pernet C, Nichols TE, Poline JB, Matthews PM, van der Lugt A, Mackay C, Lanyon L, Mazoyer B, Boardman JP, Thompson PM, Fox N, Marcus DS, Sheikh A, Cox SR, Anblagan D, Job DE, Alexander Dickie D, Rodriguez D, Wardlaw JM

とりあえずリスト
ADNI (Weiner, 2015) http://adni.loni.usc.edu/
ENIGMA (Thompson et al., 2015) http://enigma.ini.usc.edu/
ENIGMA: data is shared between members on an ad hoc basis
BRAINS (Job et al., 2016) http://www.brainsimagebank.ac.uk/
Dementia Platform UK (DPUK) http://www.dementiasplatform.uk/
Edinburgh Birth Cohort www.ebc.ed.ac.uk
European Population Imaging Infrastructure http://populationimaging.eu/
http://www.erasmus-epidemiology.nl/research/ergo.htm
Rotterdam study (Ikram et al., 2015 ;  Hofman et al., 2015)
http://www.generationr.nl/
Generation R (Jaddoe et al., 2012)
EVA, 3-CITIES, DBGIN, BIL&GIN, i-SHARE (Alperovitch et al., 2002; Lemaitre et al., 2005; Mazoyer et al. 2016). http://www.gin.cnrs.fr/BILandGIN
http://www.three-city-study.com/the-three-city-study.php
IMAGEN http://www.imagen-europe.com/en/consortium.php
Montreal Consortium for Brain Imaging Research (Evans et al., 2012). https://www.mcgill.ca/globalhealth/international-consortium-brain-mapping
OASIS (Marcus et al., 2007b ;  Marcus et al., 2009) http://www.oasis-brains.org/
Human Connectome Project (Van Essen et al., 2013) http://www.humanconnectome.org/
HCP: open access with restricted access for sensitive data (registration and application for approval by steering committee)
Rhineland study https://www.dzne.de/en/research/research-areas/population-health-sciences/rhineland-study.html
UK Biobank (Matthews and Sudlow, 2015) http://www.ukbiobank.ac.uk/

Global Signalはノイズ？情報？

The global signal in fMRI: Nuisance or Information?
Neuroimage. 2017 Feb 14;:
Authors: Liu TT, Nalci A, Falahpour M

GlobalSignalRegressionは解析手法としてはありだけど，GSにもいろんな情報含んでるよねという煮え切らない結論。

rsfMRIのSiteEffect

http://www.sciencedirect.com/science/article/pii/S1053811917300939
もめ。

N120を確保とか，むりげー。

脳アトラス

http://www.lead-dbs.org/?page_id=1004

中でもこれが良さげ。
http://atlas.brainnetome.org/download.html
264領域。
帯状回がもちっと細かいとベストなんだけどな。
AALが帯状回を3つに分けているところを7つに分割だから十分かなー。
Insulaは細かくて非常によい。
海馬の前後で分割。

動的機能的結合

The dynamic functional connectome: State-of-the-art and perspectives.
Neuroimage. 2016 Dec 26;:
Authors: Preti MG, Bolton TA, Ville DV

れびゅー。

自分のデータでは動的機能結合はうまくいかず。
実験デザインを結構選びそう。

潜在的落とし穴

Potential pitfalls when denoising resting state fMRI data using nuisance regression.
Neuroimage. 2016 Dec 23;:
Authors: Bright MG, Tench CR, Murphy K

イワーク
•Pre-whitening should be used in nuisance regression of resting state fMRI data.
•Incorporating temporal filtering into GLM accounts for changed degrees of freedom.
•Temporally shifting of nuisance regressors is sometimes warranted and advised.
•Optimal temporal shifts may not be reliably estimated from resting state data.
•Established nuisance regressors should be routinely assessed in new datasets.
とのこと。

最近論文チェックもままならず。

機能的結合は神経活動起源

Proc Natl Acad Sci U S A. 2016 Dec 14. pii: 201525369. [Epub ahead of print]
Resting-state hemodynamics are spatiotemporally coupled to synchronized and symmetric neural activity in excitatory neurons.
Ma Y, Shaik MA, Kozberg MG, Kim SH, Portes JP, Timerman D, Hillman EM.

"We show that resting-state hemodynamics can be predicted from spontaneous neural activity and correspond to a series of driven increases in local blood volume, coupled with spontaneous, bilaterally symmetric fluctuations in excitatory neural activity. This result provides reassurance that resting-state functional connectivity has neural origins. "

だとさ。
よかったよかった。

ICAによるノイズ除去

Hand classification of fMRI ICA noise components.
Griffanti L, Douaud G, Bijsterbosh J, Evangelisti S, Alfaro-Almagro F, Glasser MF, Duff EP, Fitzgibbon S, Westphal R, Carone D, Beckmann CF, Smith SM.
Neuroimage. 2016 Dec 15. pii: S1053-8119(16)30758-3. doi: 10.1016/j.neuroimage.2016.12.036.

論文そのものにアクセスできるようになってからPubmedに登録してよー

領域の活動と結合の双方を考慮した解析

https://arxiv.org/pdf/1611.07962v1.pdf

マルチサイトの信頼性

Multisite Reliability of MR-Based Functional Connectivity.
Neuroimage. 2016 Oct 13;:
Authors: Noble S, Scheinost D, Finn ES, Shen X, Papademetris X, McEwen SC, Bearden CE, Addington J, Goodyear B, Cadenhead KS, Mirzakhanian H, Cornblatt BA, Olvet DM, Mathalon DH, McGlashan TH, Perkins DO, Belger A, Seidman LJ, Thermenos H, Tsuang MT, van Erp TG, Walker EF, Hamann S, Woods SW, Cannon TD, Constable RT


•fcMRI (seed, matrix, ICD) is stable across 8 sites in a Traveling Subjects dataset.
•No major site, scanner manufacturer, or day-of-scan effects were found (GLM).
•No outlier sites were found (leave-one-site-out analysis of variance).
•Reliability substantially improves when averaging data over multiple days.
•Data can be combined across sites to increase power without impacting reliability.

だとさ。

NITRC image repository

The NITRC image repository.
Kennedy DN, Haselgrove C, Riehl J, Preuss N, Buccigrossi R.
Neuroimage. 2016 Jan 1;124(Pt B):1069-73. doi: 10.1016/j.neuroimage.2015.05.074. Epub 2015 Jun 2.

" Currently hosting 14 projects, 6845 subjects, and 8285 MRIimaging sessions, NITRC-IR provides a large array of structural, diffusion and resting state MRI data."

もめーん。

前処理

Resting-state test-retest reliability of a priori defined canonical networks over different preprocessing steps.
Brain Struct Funct. 2016 Aug 22;
Authors: Varikuti DP, Hoffstaedter F, Genon S, Schwender H, Reid AT, Eickhoff SB

いまいちすっきりしない結果。

灰白質の群平均に基づくマグキングがいいかも。
PCAデノイズもいいかも。
グローバルシグナル除去は再テストの信頼性はあがるけど，いろいろ疑義もあるよね。

って感じ。

もめーん

Reporting of Resting State fMRI Preprocessing Methodologies.
Brain Connect. 2016 Aug 9;
Authors: Waheed SH, Mirbagheri S, Agarwal S, Kamali A, Yahyavi-Firouz-Abadi N, Chaudhry A, DiGianvittorio M, Gujar SK, Pillai JJ, Sair HI


A simple but useful way to assess fMRI scan qualities.
Neuroimage. 2016 Aug 7;
Authors: Power JD

れびゅー

Brain networks under attack: robustness properties and the impact of lesions
Hannelore Aerts,1 Wim Fias,2 Karen Caeyenberghs3 and Daniele Marinazzo1

つんどく。
図がよさげ。