Normative Connectomes Leadmapper
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Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
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On the large scale of studying dynamics with MEG: Lessons learned from the Hu...
As part of the Human Connectome Project (HCP), which includes high-quality fMRI, anatomical MRI, DTi and genetic data from 1200 subjects, we have scanned and investigated a subset of 100 subjects (mostly comprised of pairs of twins) using MEG. The raw data acquired in the HCP has been analyzed using standard pipelines [ref1] and both raw and results at various levels of processing have been shared though the ConnectomeDB [ref2].
Throughout the process of the HCP we have not only analyzed (resting state) MEG data, but also have developed the data analysis protocols, the software and the strategies to achieve reproducible MEG connectivity results. The MEG data analysis software is based on FieldTrip, an open source toolbox [ref3], and is shared alongside the data to allow the analyses to be repeated on independent data.
In this presentation I will outline what the HCP MEG team has learned along the way and I will provide recommendations on what to do and what to avoid in making MEG studies on (resting state) connectivity more reproducible.
1. Larson-Prior LJ, Oostenveld R, Della Penna S, Michalareas G, Prior F, Babajani-Feremi A, Schoffelen JM, Marzetti L, de Pasquale F, Di Pompeo F, Stout J, Woolrich M, Luo Q, Bucholz R, Fries P, Pizzella V, Romani GL, Corbetta M, Snyder AZ; WU-Minn HCP Consortium. Adding dynamics to the Human Connectome Project with MEG. Neuroimage, 2013.
doi:10.1016/j.neuroimage.2013.05.056
2. Hodge MR, Horton W, Brown T, Herrick R, Olsen T, Hileman ME, McKay M, Archie KA, Cler E, Harms MP, Burgess GC, Glasser MF, Elam JS, Curtiss SW, Barch DM, Oostenveld R, Larson-Prior LJ, Ugurbil K, Van Essen DC, Marcus DS. ConnectomeDB-Sharing human brain connectivity data. Neuroimage, 2016. doi:10.1016/j.neuroimage.2015.04.046
3. Oostenveld R, Fries P, Maris E, Schoffelen JM. FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data. Comput Intell Neurosci. 2011. doi:10.1155/2011/156869
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Throughout the process of the HCP we have not only analyzed (resting state) MEG data, but also have developed the data analysis protocols, the software and the strategies to achieve reproducible MEG connectivity results. The MEG data analysis software is based on FieldTrip, an open source toolbox [ref3], and is shared alongside the data to allow the analyses to be repeated on independent data.
In this presentation I will outline what the HCP MEG team has learned along the way and I will provide recommendations on what to do and what to avoid in making MEG studies on (resting state) connectivity more reproducible.
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To help our scientists integrate all of this information and make targeted decisions, we have used Spark on Azure Databricks to build a knowledge graph of biological insights and facts. The graph powers a recommendation system which enables any AZ scientist to generate novel target hypotheses, for any disease, leveraging all of our data.
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Linear Transformations
This document discusses linear deformations and basic volumetric imaging concepts relevant to Lead-DBS workflows. It describes how linear (affine) transformations can be used to register different images of the same subject by preserving properties like parallel lines and ratios between points. These transformations map between voxel and world coordinate systems using transformation matrices stored in image headers. Rigid and affine transformations involving translation, rotation, scaling, and shearing are presented for realigning one image to another. Hands-on examples for importing and co-registering images are also mentioned.
Electrode Reconstructions VTA Modelling
Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
Discriminative Tracts
This document discusses connectomic deep brain stimulation and summarizes recent findings. It describes a tract commonly seen in STN-DBS and ALIC-DBS that traverses within the anterior limb of the internal capsule (ALIC). While this tract was previously referred to as the medial forebrain bundle (MFB), the document argues it is not the MFB but is similar to the "sl-MFB." Connectivity to medial and lateral prefrontal cortices and a potential hyperdirect pathway from the dorsal anterior cingulate cortex are discussed as being important. The anterior thalamic radiation (ATR) is also potentially linked.
Structural Connectomics dMRI
Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
Connectomic Deep Brain Stimulation
Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
Nonlinear Deformations Atlases Spaces and Advanced Concepts
Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
Function & Anatomy of the Basal Ganglia
Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
Introduction to Lead-DBS
Part of the Workshop Materials of the Lead-DBS workshop held 02/2020 in Brisbane. More information about Lead-DBS can be found here: www.lead-dbs.org
Empowering tools for Neuroimaging
This document summarizes several online tools for neuroimaging and scientific communication. It describes tools for visualizing large datasets like MicroDraw and Neuroglancer. It also outlines tools for collaboration such as Brain Box and Open Neuro Lab. Additionally, it discusses tools for publishing and organizing research like OSF, BioRxiv, Papers, and Figshare. Finally, the document presents tools for communication and project management, including ResearchGate, Github, Slack, and Trello.
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Nonlinear Deformations Atlases Spaces and Advanced Concepts
Nonlinear Deformations Atlases Spaces and Advanced Concepts
Recently uploaded
Farming systems analysis: what have we learnt?.pptx
Presentation given at the official farewell of Prof Ken Gillet at Wageningen on 13 June 2024
Methods of grain storage Structures in India.pdf
•Post-harvestlossesaccountforabout10%oftotalfoodgrainsduetounscientificstorage,insects,rodents,micro-organismsetc.,
•Totalfoodgrainproductioninindiais311milliontonnesandstorageis145mt.InIndia,annualstoragelosseshavebeenestimated14mtworthofRs.7,000croreinwhichinsectsaloneaccountfornearlyRs.1,300crores.
•InIndiaoutofthetotalproduction,about30%ismarketablesurplus
•Remaining70%isretainedandstoredbyfarmersforconsumption,seed,feed.Hence,growerneedstoragefacilitytoholdaportionofproducetosellwhenthemarketingpriceisfavourable
•TradersandCo-operativesatmarketcentresneedstoragestructurestoholdgrainswhenthetransportfacilityisinadequate
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a ∼ 106M⊙ black hole (BH) that is currently in the process of ‘turning on’. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1−W2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux ∼ 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a ∼ 106M⊙ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: active– accretion, accretion discs– galaxies: individual: SDSS J133519.91+072807.4
Post translation modification by Suyash Garg
overview of PTM helps to the students who wants to clear their basics about it.
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Magmatic iron-meteorite parent bodies are the earliest planetesimals in the Solar System,and they preserve information about conditions and planet-forming processes in thesolar nebula. In this study, we include comprehensive elemental compositions andfractional-crystallization modeling for iron meteorites from the cores of five differenti-ated asteroids from the inner Solar System. Together with previous results of metalliccores from the outer Solar System, we conclude that asteroidal cores from the outerSolar System have smaller sizes, elevated siderophile-element abundances, and simplercrystallization processes than those from the inner Solar System. These differences arerelated to the formation locations of the parent asteroids because the solar protoplane-tary disk varied in redox conditions, elemental distributions, and dynamics at differentheliocentric distances. Using highly siderophile-element data from iron meteorites, wereconstruct the distribution of calcium-aluminum-rich inclusions (CAIs) across theprotoplanetary disk within the first million years of Solar-System history. CAIs, the firstsolids to condense in the Solar System, formed close to the Sun. They were, however,concentrated within the outer disk and depleted within the inner disk. Future modelsof the structure and evolution of the protoplanetary disk should account for this dis-tribution pattern of CAIs.
fermented food science of sauerkraut.pptx
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一比一原版美国佩斯大学毕业证如何办理
原版一模一样【微信：741003700 】【美国佩斯大学毕业证成绩单】【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
【主营项目】
一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！
二.真实使馆公证(即留学回国人员证明,不成功不收费)
三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）
四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度)
如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
◇面对父母的压力，希望尽快拿到；
◇不清楚认证流程以及材料该如何准备；
◇回国时间很长，忘记办理；
◇回国马上就要找工作，办给用人单位看；
◇企事业单位必须要求办理的
◇需要报考公务员、购买免税车、落转户口
◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
办理美国佩斯大学毕业证【微信：741003700 】外观非常简单，由纸质材料制成，上面印有校徽、校名、毕业生姓名、专业等信息。
办理美国佩斯大学毕业证【微信：741003700 】格式相对统一，各专业都有相应的模板。通常包括以下部分：
校徽：象征着学校的荣誉和传承。
校名:学校英文全称
授予学位：本部分将注明获得的具体学位名称。
毕业生姓名：这是最重要的信息之一，标志着该证书是由特定人员获得的。
颁发日期：这是毕业正式生效的时间，也代表着毕业生学业的结束。
其他信息：根据不同的专业和学位，可能会有一些特定的信息或章节。
办理美国佩斯大学毕业证【微信：741003700 】价值很高，需要妥善保管。一般来说，应放置在安全、干燥、防潮的地方，避免长时间暴露在阳光下。如需使用，最好使用复印件而不是原件，以免丢失。
综上所述，办理美国佩斯大学毕业证【微信：741003700 】是证明身份和学历的高价值文件。外观简单庄重，格式统一，包括重要的个人信息和发布日期。对持有人来说，妥善保管是非常重要的。
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
Ahota Beel, nestled in Sootea Biswanath Assam , is celebrated for its extraordinary diversity of bird species. This wetland sanctuary supports a myriad of avian residents and migrants alike. Visitors can admire the elegant flights of migratory species such as the Northern Pintail and Eurasian Wigeon, alongside resident birds including the Asian Openbill and Pheasant-tailed Jacana. With its tranquil scenery and varied habitats, Ahota Beel offers a perfect haven for birdwatchers to appreciate and study the vibrant birdlife that thrives in this natural refuge.
Anti-Universe And Emergent Gravity and the Dark Universe
Recent theoretical progress indicates that spacetime and gravity emerge together from the entanglement structure of an underlying microscopic theory. These ideas are best understood in Anti-de Sitter space, where they rely on the area law for entanglement entropy. The extension to de Sitter space requires taking into account the entropy and temperature associated with the cosmological horizon. Using insights from string theory, black hole physics and quantum information theory we argue that the positive dark energy leads to a thermal volume law contribution to the entropy that overtakes the area law precisely at the cosmological horizon. Due to the competition between area and volume law entanglement the microscopic de Sitter states do not thermalise at sub-Hubble scales: they exhibit memory effects in the form of an entropy displacement caused by matter. The emergent laws of gravity contain an additional ‘dark’ gravitational force describing the ‘elastic’ response due to the entropy displacement. We derive an estimate of the strength of this extra force in terms of the baryonic mass, Newton’s constant and the Hubble acceleration scale a0 = cH0, and provide evidence for the fact that this additional ‘dark gravity force’ explains the observed phenomena in galaxies and clusters currently attributed to dark matter.
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptx
Centrifugation is a powerful technique used in laboratories to separate components of a heterogeneous mixture based on their density. This process utilizes centrifugal force to rapidly spin samples, causing denser particles to migrate outward more quickly than lighter ones. As a result, distinct layers form within the sample tube, allowing for easy isolation and purification of target substances.
Quality assurance B.pharm 6th semester BP606T UNIT 5
Warehousing
Good warehousing practices
Material management
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...
We present the JWST discovery of SN 2023adsy, a transient object located in a host galaxy JADES-GS
+
53.13485
−
27.82088
with a host spectroscopic redshift of
2.903
±
0.007
. The transient was identified in deep James Webb Space Telescope (JWST)/NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) program. Photometric and spectroscopic followup with NIRCam and NIRSpec, respectively, confirm the redshift and yield UV-NIR light-curve, NIR color, and spectroscopic information all consistent with a Type Ia classification. Despite its classification as a likely SN Ia, SN 2023adsy is both fairly red (
�
(
�
−
�
)
∼
0.9
) despite a host galaxy with low-extinction and has a high Ca II velocity (
19
,
000
±
2
,
000
km/s) compared to the general population of SNe Ia. While these characteristics are consistent with some Ca-rich SNe Ia, particularly SN 2016hnk, SN 2023adsy is intrinsically brighter than the low-
�
Ca-rich population. Although such an object is too red for any low-
�
cosmological sample, we apply a fiducial standardization approach to SN 2023adsy and find that the SN 2023adsy luminosity distance measurement is in excellent agreement (
≲
1
�
) with
Λ
CDM. Therefore unlike low-
�
Ca-rich SNe Ia, SN 2023adsy is standardizable and gives no indication that SN Ia standardized luminosities change significantly with redshift. A larger sample of distant SNe Ia is required to determine if SN Ia population characteristics at high-
�
truly diverge from their low-
�
counterparts, and to confirm that standardized luminosities nevertheless remain constant with redshift.
Recently uploaded (20)
Farming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptx
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Microbiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Anti-Universe And Emergent Gravity and the Dark Universe
Anti-Universe And Emergent Gravity and the Dark Universe
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptx
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptx
Quality assurance B.pharm 6th semester BP606T UNIT 5
Quality assurance B.pharm 6th semester BP606T UNIT 5
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...
Normative Connectomes Leadmapper
- 1. USING NORMATIVE CONNECTOMES TO ANALYZE DATA IN LEAD CONNECTOME MAPPER LEAD-DBS WORKSHOP QUEENSLAND| FEB 2020 | Friederike Irmen
- 2. friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS The use of normative connectomes Irmen et al., AoN, in revision Li et al., submitted Elias et al. (2020), Brain Stim
- 3. Why normative connectomes? • After DBS surgery, patients cannot be scanned in the MRI without restrictions, acquiring high quality data is difficult if not impossible • Normative connectomes: “average wiring diagrams” of the human brain • Based on diffusion-weighted or resting-state functional MRI • Advantages: Recorded on specialized MRI hardware, high signal- to-noise ratio, large samples friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 4. friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 5. friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 6. friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 7. • Select patient folders friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 8. Connectivity from seeds or connectivity matrices Select the connectome (and resolution) friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 9. Connectivity map from seed • Connectivity seeding from VTAs of each patient • Based on the normative connectome data for healthy subjects or e.g. PD patients • Calculation may take a while friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 10. Example: calculate functional connectivity profile based on PD connectome friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 11. • Files generated: Example: calculate functional connectivity profile based on PD connectome friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 12. friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 13. Other options • Select BER001-BER003 • Generate a connectivity matrix for the VTA contacts and the other voxels in the connectivity map • Export time series of patients within all the connected voxels friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 14. v friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 15. Create a folder with specific patient files/VTAs friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 16. friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 17. Results friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
- 18. fMRI-based connectivity from BER001, BER002, BER003 to the depression network, could be correlated e.g. with depression score friederike.irmen@charite.deLead-DBS Workshop Normative connectomic analyses in Lead-DBS
Editor's Notes
- In their work, Li et al. compare two different patient cohorts undergoing DBS for treatment resistant obsessive compulsive disorder (OCD) from two study centers, Grenoble (n = 14) and Cologne (n = 22) with DBS in two different brain targets, the anteromedial subthalamic nucleus (amSTN) in Grenoble and the anterior limb of the internal capsule = ALIC in Cologne