backtracking algorithm
Implement this in nipype/niflows
75 Matching Annotations
- May 2018
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www.pnas.org www.pnas.org
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MT
Magnetization transfer
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www.nature.com www.nature.com
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Before reproducibility must come preproducibility
This article touches on many components of the repronim project.
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www.pnas.org www.pnas.org
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Adolescence is associated with genomically patternedconsolidation of the hubs of the humanbrain connectome
First repropaper example
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group.springernature.com group.springernature.com
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Researchers’ challenges in sharing data cross geographic borders and disciplines
Another report on challenges in data sharing.
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- Jan 2018
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arxiv.org arxiv.org
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Accurate autocorrelation modeling substantially improvesfMRI reliability
Considering the availability of code and a comparative workflow, this would be a likely candidate for the ReproPaper Initiative.
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- Sep 2017
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www.biorxiv.org www.biorxiv.org
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10datasetscompris-ing2,295subjectswith2,861scans
perhaps list these are public datasets. i had to look at m2g to figure out.
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whicharenowpubliclyavailable
Perhaps list m2g.io over here as well.
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accurate
Since there is no ground truth, how can accuracy be evaluated?
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slightlyimprovedorsignificantlydeterioratedperformance
How was performance evaluated? Was there an objective method to determine this? Given the different choices of nonlinear registration methods, was ANTs and other tools evaluated.
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- Aug 2017
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mbakker7.github.io mbakker7.github.io
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Exploratory computing with Python
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github.com github.comd3/d31
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Gallery
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www.interaction-design.org www.interaction-design.org
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The Properties of Human Memory and Their Importance for Information Visualization
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www.informationisbeautiful.net www.informationisbeautiful.net
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About
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journal.frontiersin.org journal.frontiersin.org
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When Null Hypothesis Significance Testing Is Unsuitable for Research: A Reassessment
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- Jan 2017
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www.nature.com www.nature.com
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Replication studies offer much more than technical details
Another editorial highlighting that highlights the merits of replication beyond repeat and raises questions about the culture of science and confirmation bias.
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- Nov 2016
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stepik.org stepik.org
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We are open for knowledge
just came across this platform. It's used in PyCharm to provide Python tutorial functionality.
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www.w3.org www.w3.org
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Data on the Web Best Practices
A description for different qualities and targets for data sharing or publishing.
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samnicholls.net samnicholls.net
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Bioinformatics is a disorganised disaster and I am too. So I made a shell.
This is a shell-wrapper to minimize the effort needed to collect command line provenance.
This post covers a lot of ground to describe practical and human requirements.
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www.software.ac.uk www.software.ac.uk
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Top ten reasons to not share your code (and why you should anyway)
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- Oct 2016
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linkeddatabook.com linkeddatabook.com
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Linked Data: Evolving the Web into a Global Data Space
A comprehensive book on linked data.
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www.datacarpentry.org www.datacarpentry.org
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Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research.
Training for data skills
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www.wings-workflows.org www.wings-workflows.org
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WINGS is a semantic workflow system
A meta level representation of workflows.
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- Sep 2016
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www.pachyderm.io www.pachyderm.io
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A Containerized Data Lake
A data container + workflow spec
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github.com github.com
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duecredit/duecredit
A Python library to include citations in your python software packages.
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aws.amazon.com aws.amazon.com
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CfnCluster
Amazon's own product similar to starcluster.
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dataverse.harvard.edu dataverse.harvard.edu
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Brain Genomics Superstruct Project (GSP)
License: Data use agreement Access: Human, API Needs data use agreement: Yes Needs institutional signature for access: No
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studyforrest.org studyforrest.org
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What is studyforrest?
Rich multimodal dataset on naturalistic stimuli
- License: PDDL v.10
- Access: Human, rsync, git annex
- Needs data use agreement: No
- Needs institutional signature for access: No
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- Aug 2016
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fivethirtyeight.com fivethirtyeight.com
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Science Isn’t Broken
A nice tool that illustrates the impact of being able to continuously run tests.
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journals.plos.org journals.plos.org
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Ten Simple Rules for Effective Statistical Practice
A very nice overview of things to keep in mind when designing experiments and analyzing data with statistics
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garstats.wordpress.com garstats.wordpress.com
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Robust effect sizes for 2 independent groups
A nice treatise on how to measure effect sizes robustly
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fivethirtyeight.com fivethirtyeight.com
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Not Even Scientists Can Easily Explain P-values
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library.mpib-berlin.mpg.de library.mpib-berlin.mpg.de
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Th e Null Ritual What You Always Wanted to Know About Signifi cance Testing but Were Afraid to Ask
Understanding null hypothesis testing and considering alternatives
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neurohackweek.github.io neurohackweek.github.io
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Lesson template for Neurohackweek
A GitHub template for creating lesson plans. While this doesn't provide the flexibility of a computational environment within this lesson plan, it serves as a good approach to outline concepts of lessons.
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www.nature.com www.nature.com
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replication ecosystem, such as it is, lacks visibility, value and conventions.
a key social concern
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www.kaggle.com www.kaggle.com
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Welcome to Kaggle Datasets
Kaggle now allows publish datasets. It will be interesting to investigate what kind of datasets are allowed and how it captures metadata.
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waffle.io waffle.io
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Smart & Simple Project Management
another project management solution for GitHub and it appears to be free. i may replace zenhub with this.
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- Jul 2016
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nautil.us nautil.us
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We Should Not Accept Scientific Results That Have Not Been Repeated
A nice article on reproducibility and need for structural change in science.
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dat-data.com dat-data.comdat1
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The Dat Project
A peer-to-peer data distribution service
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learningequality.org learningequality.org
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An offline version of Khan Academy.
A lightweight deployable platform for teaching from khan academy.
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www.cambridgesemantics.com www.cambridgesemantics.com
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A beginner's introduction to Semantic Web and Linked Data.
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Openness is a core value of scientific practice.
A set of badges to tag open science.
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try.github.io try.github.ioTry Git1
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Got 15 minutes and want to learn Git?
A tutorial from GitHub to learn git.
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URL
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- Jun 2016
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www.nih.gov www.nih.govTraining1
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Training
NIH efforts towards reproducibility. This includes videos for training and discussion material as well.
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cds.nyu.edu cds.nyu.edu
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ReproZip
a python framework for packaging experiments for publication
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rr-project.org rr-project.org
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rr
record and replay application
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bitbucket.org bitbucket.org
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smtp: mail.server
this doesn't matter
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- May 2016
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www.nomadproject.io www.nomadproject.io
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Easily deploy applications at any scale
A modern distributed scheduler
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www.nature.com www.nature.com
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Reality check on reproducibility
Survey about the state of reproducibility
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www.google.com www.google.com
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Course Builder
tool to create courses
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www.zenhub.io www.zenhub.io
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Manage projects without leaving GitHub.
another trello like project management system integrated with github.
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wekan.io wekan.io
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The open-source Trello-like kanban
opensource trello like platform
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sandstorm.io sandstorm.io
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Sandstorm
an opensource framework for app distribution. list of apps at:
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bitesizebio.com bitesizebio.com
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this is relevant to training
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- Feb 2016
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github.com github.com
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the ants registration can be made more robust by removing the Translate transform and using use initial_moving transform. i do like the transform parameters here:
https://github.com/nipy/nipype/blob/master/examples/fmri_ants_openfmri.py#L202
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datasource can be combined into a single datagrabber. along the lines here: https://github.com/nipy/nipype/blob/master/examples/fmri_ants_openfmri.py#L667
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- Jun 2014
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github.com github.com
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our
Our
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For example, slicing a set of ordered series data by rows (spectral dimension) and columns (temporal dimension) is quite simple:
This is indeed a simple example. However, could you provide a few non-trivial use cases that are made really simple?
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Top: Absorbance
These figures are also missing axes labels.
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The simulation codebase may be found
Include this link in the abstract/introduction.
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Temporal evolution
Figures have no labeling on the axes.
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relevant plasmonic
relevant to plasmonic
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Despite these benefits, nanobiosensing research in general is faced with several hinderances.
Despite these benefits, several issues impede nanobiosensing research.
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A Computational Framework for Plasmonic Nanobiosensing
Quality of the approach: meets Quality of the writing: meets Quality of the figures/tables: below
Is the code made publicly available and does the article sufficiently describe how to access it?
yes
Does the article present the problem in an appropriate context? Specifically, does it:
- explain why the problem is important --> yes
- describe in which situations it arises --> yes outline relevant previous work -> cannot judge provide background information for non-experts -> yes
Is the content of the paper accessible to a computational scientist with no specific knowledge in the given field?
the article does provide some background that made it easier for me to follow, but i simply do not have expertise in the underlying domain.
Does the paper describe a well-formulated scientific or technical achievement?
appears to.
Are the technical and scientific decisions well-motivated and clearly explained? Are the code examples (if any) sound, clear, and well-written?
these are primarily driven by the need for a simple way to interact with the sensors.
Is the paper factual correct? Is the language and grammar of sufficient quality?
there are a few typos that i have noted, but otherwise yes.
Are the conclusions justified?
yes - from the perspective of simplicity.
Is prior work properly and fully cited?
i cannot comment on this.
Should any part of the article be shortened or expanded? Please explain. In your view, is the paper fit for publication in the conference proceedings? Please suggest specific improvements and indicate whether you think the article needs a significant rewrite (rather than a minor revision).
yes
- explain why the problem is important --> yes
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github.com github.com
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amg_cycle
docstring - also use of
execis not recommended. please expand parameters into keyword args. -
iterative_solve
docsting
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coarsen_A(
docstring
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def restriction(N, shape):
Add comment describing what this function does and what the parameters do
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restrictions
missing docstring here
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coarse point nearest to the camera in the bottom
perhaps indicate this explicitly in the figure
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OpenMG: A New Multigrid Implementation in Python
Quality of the approach: meets Quality of the writing: meets Quality of the figures/tables: meets
Is the code made publicly available and does the article sufficiently describe how to access it? yes
Does the article present the problem in an appropriate context? Specifically, does it:
- explain why the problem is important --> yes
- describe in which situations it arises --> yes
- outline relevant previous work -> some, cannot judge full extent
- provide background information for non-experts -> yes
Is the content of the paper accessible to a computational scientist with no specific knowledge in the given field?
the article does provide some background that made it easier for me to follow, but i do not have sufficient expertise in Galerkin discretization approaches, but the general idea of using multi resolution solvers to iteratively approximate the true solution was conveyed in the article.
Does the paper describe a well-formulated scientific or technical achievement?
yes
Are the technical and scientific decisions well-motivated and clearly explained? Are the code examples (if any) sound, clear, and well-written?
yes. the code examples can be improved with better Python standards as noted.
Is the paper factual correct? Is the language and grammar of sufficient quality? Are the conclusions justified?
yes
Is prior work properly and fully cited?
i cannot comment on this.
Should any part of the article be shortened or expanded? Please explain. In your view, is the paper fit for publication in the conference proceedings? Please suggest specific improvements and indicate whether you think the article needs a significant rewrite (rather than a minor revision).
yes
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OpenMG
include URL here
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overall accuracy
how is accuracy evaluated? is it simply || Au^\hat - b ||_2?
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web.hypothes.is web.hypothes.is
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Imagine
showing a demo of hypthesis at brainhack
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- Feb 2014
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brainspell.org brainspell.org
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satra (LOG OUT) NEWS ABOUT DOWNLOAD CHANGES OF BRAIN ACTIVATION PRE- POST SHORT-TERM PSYCHODYNAMIC INPATIENT PSYCHOTHERAPY: AN FMRI STUDY OF PANIC DISORDER PATIENTS. Beutel ME, Stark R, Pan H, Silbersweig D, Dietrich S (2010) Psychiatry Res 184(2):96-104 [PubMed] [Neurosynth] [Full Text] Cognitive-behavioural interventions have been shown to change brain functioning. We used an emotional linguistic go/nogo functional magnetic resonance imaging (fMRI) design to determine changes of brain activation patterns of panic disorder (PD) patients following short-term psychodynamic inpatient treatment. Nine PD patients underwent fMRI before and after treatment; 18 healthy controls were scanned twice at the same interval (4 weeks). In the go/nogo design, responses to panic-specific negative words were compared with linguistically matched positive and neutral words. According to hypotheses, patients rated affective words more strongly than controls and selectively recalled negative vs. positive/neutral words. Before treatment, high limbic (hippocampus and amygdala) activation was accompanied by low prefrontal activation to negative words. Inhibition-related activation patterns indicated difficulties of behavioural regulation in emotional context. At treatment termination, panic-related symptoms had improved significantly, and fronto-limbic activation patterns were normalized. Our results indicate that short-term psychodynamic treatment leads to changes in fronto-limbic circuitry not dissimilar to previous findings on cognitive-behavioural treatments. Metadata MeSH descriptors BrainBrain MappingEmotionsFemaleHumansImage Processing, Computer-AssistedInhibition (Psychology)InpatientsMagnetic Resonance ImagingMaleNeuropsychological TestsPanic DisorderPsychotherapy, BriefTreatment Outcome Stereotaxic space MNI Talairach Number of subjects Experiments Title:(Empty) Caption:(Empty) X Y Z -23 -17 -9 -23 -17 -9 -23 -17 -9 -23 -11 -9 -23 -11 -9 -23 -11 -9 -60 -54 2 -60 -54 2 -60 -54 2 46 14 17 46 14 17 46 14 17 -20 -11 -9 -20 -11 -9 -20 -11 -9 -20 -14 -11 -20 -14 -11 -20 -14 -11 26 -19 -6 26 -19 -6 26 -19 -6 -14 -15 23 -14 -15 23 -14 -15 23 -43 1 24 -43 1 24 -43 1 24 -43 0 26 -43 0 26 -43 0 26 -41 41 -6 -41 41 -6 -41 41 -6 +Cognitive Atlas Tasks +Cognitive Atlas Cognitive Domains +BrainMap Behavioural Domains Table is correct No Discussion roberto (12/31/2013 8:09:11 AM) Locations in the 1st experiment are each repeated 3 times Post your comment brainspell by Roberto Toro is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
these rows are replicated
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