Reproducibility in Neuroscience  A best practice example
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Reproducibility in Neuroscience  A best practice example

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CC Attribution  NoDerivatives 3.0 Germany:
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2019

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English

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Abstract 
Reproducibility in Neuroscience  A best practice example The last decade has seen intensive discussions on reproducibility in the analysis of neuroimaging experiments. This has lead to efforts in the neuroscience community in various directions, e.g., accessibility of 'minimally processed image and metadata' from large studies for scientific purposes public data archives open data standards open source software and analysis pipelines. This enables, e.g., the development of best practice analysis strategies combination of findings from different studies test of and comparisons with alternative modeling approaches I'll discuss how this fits, as a best practice example, into the current discussions on reproducibility of research and (open) research data.

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Statistics
Special unitary group
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Observational study
Table (information)
Formal power series
Standard error
Statistics
Mortality rate
Hypothesis
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Goodness of fit
Observational study
Standard error
Formal power series
Table (information)
Manysorted logic
Relation <Mathematik>
Limit (category theory)
Statistics
Total S.A.
Mortality rate
Hypothesis
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Statistics
Observational study
Standard error
Table (information)
Observational study
Limit (category theory)
Statistics
Mortality rate
Hypothesis
Formal power series
Relation <Mathematik>
Modulform
Gamma function
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Group action
Observational study
Standard error
Formal power series
Table (information)
Observational study
Relation <Mathematik>
Limit (category theory)
Statistics
Mortality rate
Grothendieck topology
Hypothesis
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Statistical hypothesis testing
Observational study
Standard error
Table (information)
Observational study
Closed set
Sampling (statistics)
Statistics
Event horizon
Mortality rate
Hypothesis
Power (physics)
Formal power series
Manysorted logic
Relation <Mathematik>
Maß <Mathematik>
03:26
Group action
Sine
Observational study
Table (information)
Standard error
Observational study
Mass flow rate
Decision theory
Dreizehn
Total S.A.
Statistics
Mortality rate
Hypothesis
Formal power series
Hill differential equation
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Observational study
Mathematical analysis
Analytic set
Hypothesis
Power (physics)
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Population density
Group action
Observational study
Observational study
Autoregressive conditional heteroskedasticity
Mathematical analysis
Analytic set
Numerical analysis
Hypothesis
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Population density
Observational study
Observational study
Different (Kate Ryan album)
Mathematical analysis
Set (mathematics)
Analytic set
Hypothesis
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Explosion
Population density
Observational study
Observational study
Analytic set
Hypothesis
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Statistical hypothesis testing
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Statistics
Observational study
Multiplication sign
Analytic set
Grothendieck topology
Mach's principle
Exclusive or
Manysorted logic
Natural number
Determinant
Randomization
Standard deviation
Observational study
Link (knot theory)
Validity (statistics)
Physical law
Model theory
Independence (probability theory)
Parameter (computer programming)
Lattice (order)
Statistics
Hypothesis
Population density
Sample (statistics)
Coefficient of determination
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Observational study
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Sine
Equals sign
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Point (geometry)
Cartesian coordinate system
Grothendieck topology
Open set
Power (physics)
Numerical analysis
Sign (mathematics)
Population density
Coefficient
Estimation
Crosscorrelation
Diagonal
Design of experiments
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Observational study
State of matter
Parametrische Erregung
Multiplication sign
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Graph coloring
Coefficient
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Multiplication
Mathematical optimization
Position operator
Observational study
Sine
Statistical dispersion
Point (geometry)
Mathematical analysis
Parameter (computer programming)
Total S.A.
Set (mathematics)
Binary file
Evolute
Grothendieck topology
Open set
Estimation
Crosscorrelation
Diagonal
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Database normalization
Sign (mathematics)
Observational study
Parametrische Erregung
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Moving average
Funktionalanalysis
Mathematical analysis
Open set
Statistics
Physical system
Condition number
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Funktionalanalysis
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Funktionalanalysis
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Moving average
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Explosion
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INTEGRAL
Data analysis
Lattice (order)
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Mach's principle
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Explosion
Mass flow rate
Multiplication sign
Data analysis
Stochastic kernel estimation
Lattice (order)
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Curve
Data analysis
Point cloud
Total S.A.
Mereology
Lattice (order)
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Counting
Lattice (order)
Open set
Computational physics
Explosion
Thermodynamisches System
Function (mathematics)
Phase transition
Connectivity (graph theory)
Normal (geometry)
Multiplication
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Mass flow rate
Observational study
Model theory
Disintegration
Algebraic structure
Kontraktion <Mathematik>
Funktionalanalysis
Mathematical analysis
Average
Normal (geometry)
Multiplication
Surjective function
Modal logic
Observational study
Group action
Statistics
Grothendieck topology
Open set
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Latent heat
Sample (statistics)
Function (mathematics)
Connectivity (graph theory)
Matrix (mathematics)
Associative property
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Modal logic
Observational study
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State of matter
Conic section
Algebraic structure
Mathematical analysis
Group action
Perspective (visual)
Function (mathematics)
Connectivity (graph theory)
Associative property
Multiplication
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Associative property
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Modal logic
Group action
Observational study
Multiplication sign
Algebraic structure
Mathematical analysis
Group action
Perspective (visual)
Different (Kate Ryan album)
Function (mathematics)
Connectivity (graph theory)
Multiplication
Associative property
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Standard deviation
Observational study
Frequency
Process (computing)
Network topology
Mathematical analysis
Open set
Identifiability
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Standard deviation
Observational study
Process (computing)
State of matter
Modal logic
Algebraic structure
Funktionalanalysis
Mathematical analysis
Open set
Mach's principle
Local Group
Frequency
Manysorted logic
Network topology
Different (Kate Ryan album)
Object (grammar)
Modulform
Identifiability
Standard deviation
Observational study
Model theory
Conic section
Algebraic structure
Data analysis
Funktionalanalysis
Set (mathematics)
Open set
Latent heat
Positional notation
Frequency
Autoregressive conditional heteroskedasticity
Object (grammar)
Experimentelle Versuchsforschung
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Point (geometry)
Network topology
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Biostatistics
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Normed vector space
Disintegration
Projective plane
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Mach's principle
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Set (mathematics)
Modal logic
Covering space
Disintegration
Parameter (computer programming)
Range (statistics)
Mathematical analysis
Open set
Different (Kate Ryan album)
Series (mathematics)
Autoregressive conditional heteroskedasticity
Physics
Modulform
Multiplication
Maß <Mathematik>
Spacetime
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and the sun Bichel way would have been to go or and talk a ball at so what we do in statistics and you wanna drink but I think that having to
00:17
look at the tell and so all the developments in AI
00:24
the new and newer sciences and tongue in you will matching could of concerning couple disability until it here I mean the producibility in the hip he cut the to get may be of more interest for of origin and audience so were that's why OK let's start with some saying
00:53
code cooperative that's this paper by you're not is slower 2005 of was starting good quite a discussion in the view
01:07
medical sciences community and that sort of has said that he did the tidal wine most published research finding off for and those what good
01:24
panted all at once there are several reasons slow for this of being 1 is mostly how that are published based on the new
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studies of them based on form statistic is in the significance so the started quite a discussion what p their
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use and It's based on publications discounting can negative besides not only per publications already the
02:00
all people who did this studies without seeking a ballot sending the 2 sides of a study to a publisher if the the sites of the wimp showing the effect so this is something that's no new and saddest
02:21
Texas publication bias and so that's put some of my skin and military 1 of from this paper and assess if you have Hi from
02:36
type 1 of 1 unit apertures testing 1 must be daft the power of further IQ tests assuming took or studies have to sample and all this stuff they shoe all of pool and find Sharaf over and forts hypothesis test that then what you get all of this sort sport potion follow CPU relationships so that that corresponding to 1 your research findings and depending on you see that close to the pop ocean follow where you have a lot of events where you have research finding yes and the
03:26
Tool relationship is known for
03:31
maybe larger than the opposite Let's continue this alienation coming in and this issue is biased new toward study design porblems and this may be that the there are problems in the the in the designs the planning because of this study there may be problems concerning economization of studies so the main media problems so that in that election the flow of this too much flexibility in the study these iron so they are decisions about how Potters's Sfard about tested mate after the study has been conducted on experiment has been conceived conducted and this and it's to another the effect that consider it you of this you know pull portion of research findings new tool study design problems that shouldn't we list as find this findings the course of past porblems in my study planning and then the city's this instigation and that's what's sin a paper on or you
05:01
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kilometers of and they stay at research findings on less likely to be cool if of the the power of the what if the better of sub describing good or that after 2nd kind of inhabitants testing get smaller the if the
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gets smaller under its effect no gifted st the size of to study gets 1 so that's so goes into battle if the
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effect of the study smaller if the number of coupled business tested gets larger but if the flexibility offered
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design and definition of alt Kong's all analytic and metal it's source used gets larger all if the financial all other interests for the off to explore mentor all of the some please settings in the mind of the interests of the community what on getting larger to conclusions as way of you have to do
06:32
large studies all all new bias meant analyzes of combining information from different studies there is a need
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for Cook Kennedy of evidence so all his studies
06:50
independently of what they hear a report by its this and this side should be published and there should be some seemed like and opt for 1 legislation of studies so that Everybody knows
07:06
how many studies where conducted and can a scene how many of these studies had a positive side OK
07:19
can of there was quite a time before the the let us we're taking so in 2014 of as an aside of meeting Gulf Shores exuded it's sort of something on of major drawn it's in biomedical sciences or finding agencies and scientific societies same this meeting was heard at the NIH and no U.S. law of was conducted and the study cited there was sold it took Tolia all published in Science at the same time in nature and the singles win some model and the John Arts the calling for what the producibility usually go on transparency and independent validation tests cornerstones of the scientific method and defining principles and guidelines for plea Clinica Medica the solche to you what they are aware of the on the boss the porting of filament of does standards that decayed statistics' economization blinding of studies so send the size determination criteria for data exclusion all this should be in the public publications they reminded the deposition of data and public with positive always and to link these they've got toward a publications and though deal of make an obligation to consider publication contradict all users of the sites in the same German 2nd the
09:20
interesting study this time from in psychology the this paper in Science compean the investigated the bold 1 hamlet to a studies in psychology for the applicability so the studies were conducted again and what you see is so bowl which no affect science and the application fixed
09:52
size and so there are studies that could be replicated in blue but were a large number of studies that could be replicated was assigned a dancer
10:05
public here in publication for conducting go to such OK for a new look at the
10:16
following you in the Chink the foster of of the study that I have found more slowly the paper by land mine in totals and 11 who conducted the of might impediment taking your limiting the publicity case study so the the teeth soul of data where our own according to the 11 different modalities in scandalously studies source scanning the same patient After soaking time again for the same subject what did for the porting of settings and at position parameters will analysis pipelines so the software published of you sort of new emission can for medics twits and resources clearing colors so that that's situated as the NIH the the data home open the variables so were suppose only and they extra seats early in college sure the use of the state for the development optimization and evolution of arrival of new within you
11:43
imaging there's quite a long time condition for the Open Software
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so the main soft then Mehlman's SunSoft that would say where I developed though within the community on now open signs the open source licenses so that's
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centers of function the image of a stop at by Cox in 1996 then there's some of national I were of medicine inside segmentation police station to a kid I ITK know the advanced normalization to words please so far it has said and status in the parliament in that the closest to name the main 2 words or the softer connections so that the home him in the when it's slow
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2 thousand 14 meeting occurred in humble IC the organization of human blend mapping curve of was addressing the Paul
12:51
Blum off Cook disability and data of integrity in our new of science we result shows misstatement of its constant and at this meeting
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could comic a comic you and best practices in data analysis and sharing of all the data in money because resonance imaging was established this comic key published of the Paltz been made to oppose in 16 so this was sort of you he
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before the 20 second or which B and we think of the comic you will see that by tonic it's a statistician at that time
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involving kernel were in ox halt and close it so appalled of a ball it the so the pages plus slow 40 pages flow for appendices and I think it's most of those leading a similar on the comedy was
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established in at the bank of meeting totals and 17 for MEG in EEG and the dinner or was
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so the called now were informal from of equipment
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OK chairman donors the Deligne now Newell image for 1 of 2 leading journalists of of You'll imaging curve published pruning special issues in totals and 16 and opposing 17 all in the the opening date down of a positive list when it's in just the long list here and what
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I I would like to do was to mention to
14:57
what the scope was it always candidate more in detail so 1 is the of
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Washington University Minnesota human comic tone of contracts of database of that's designed to of date of home several you sure the public the following that studies of some mainland
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study was so the the other human conic Thom Haugen so of imaging study 7 here on this modem would screen T. with 1 thousand 2 it's slower subjects slow of structural resting state past based Atiyah hall the data are being able to date are there will also be genomewide association data for for this of these data down how public you
16:05
available after legislation for scientific purposes and the was requires Citation of certain papers depending call
16:18
on my own which type of
16:22
data as a success than the induced there's a 2nd 1 so that the life span primary data aware of different age groups are followed so what some of the amount of time the
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segments and 1 of the
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interesting because our child is still open you will I shall have established close by him the List Stanford Center for the producer Munoz science of
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started as sort of s and deposit or leave the floor function all of the autumn from a you the positively and so now contains about 180 new imaging studies in standardized form so awkward bits format and also supplies standardized of pipelines for was has single word it out for several modalities the data are formed model knew what he can be directly downloaded you know us from that services all the likely form mod Arch of websites with this fast access to these are curious did put it include extensive of editing access can be restricted for a period of study 6 months so that's and the lesser so the Commission of the prevalence for all manner so to publisher the sides based on the data before it's so of can be publicly used though of 2 data sets needs to have necessary it takes permissions and so to share the data publicly and the data and has to be anonymous Our usually use of the state down of Simon Open Data license and clients citing couple followed the papers where on these of the data from these studies where frost used OK the bits than not
18:59
of stand not follow organization of MRI data in nifty formant that was adapted so buying Sutherland data showing could a positive ways so 1 that what Newell is 1 of the new conic Thom portrait this another 1 and this poll bordered by the committee of on best practices in data and the the CenturyLink of the human by mapping a organization the it's organized in form of of data some fauna structure and that love puts slow data for different subjects in the studies in different but actually is and then not again so but it's so of the data according to what different types so often matches the phone would entities there's a they distorts in Yau where script objection the optic mode notion or raising in finance which is close to me which a certain type of phone of text file and supplementary of information is usually and useful facts OK
20:20
that's called platform that looks like we have access to this point this
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whole of Liskov datasets looks like on the open new
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the special data sets in my Conatel data set here yesterday of society all the pieces
20:45
so aboard pipelines the
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summary of the pipeline in of the piano by ear to the public locked to 1st and fault OK what
21:00
I would so like to wasn't mentioned this to you will conduct a project that's a Pauget started by the the from the status a community in you a you a matching can and to the package developments to put Peron and college use of all and you won't get them a drink and integrates with existing all new assignments of the new imaging software and and it's complete solar
21:32
of pipelines cold it's
21:37
91 packages we always all contribute you and the last thing
21:43
I do I would like to mention this so the book portrait of that we all just impulsive softener a drink so we're sent next week toward the publish of that's about the new imaging can it provides a slow in for the coupling of the form of what men and his pipelines for different modalities of different experiments on all its space completed based on open soft now it's slower using open datasets from Auden deposit always it's completely living loutish using Canada so it's would be a dynamic of a document and that's what a economists Cauchy Center for sure the and