Preprint on functional connectivity fingerprinting

Preprint – Fingerprinting and behavioural prediction rest on distinct functional systems of the human connectome

New preprint on the relation between functional connectome-based identification and behavioural prediction! Based on high-quality resting-state fMRI, we find a dichotomy of signatures underlying the identification of individuals and the prediction of behaviour. The dichotomy is apparent on all levels of analysis, looking at individual connections, resting-state networks and topological distribution. Find the preprint here!

Preprint on functional connectivity fingerprintingNina2021-07-12T15:26:57+02:00

New article in NeuroImage: Clinical: Transdiagnostic analysis reveals a shared hippocampal damage pattern across neuroimmunological diseases

Our recent article shows that hippocampal surface deformations converge on the left anterior hippocampus in patients with multiple sclerosis, NMDA receptor encephalitis and LGI1 encephalitis. This surface area appears to be particularly vulnerable across diseases and is sensitive to cognitive alterations.

Discover the spatial patterns in our full-text here.

New article in NeuroImage: Clinical: Transdiagnostic analysis reveals a shared hippocampal damage pattern across neuroimmunological diseasesNina2021-01-15T11:53:50+01:00

New members joining our lab!

We are happy to announce that four new members are joining our lab.

Katia Schwichtenberg will be working for her medical doctoral project in 2021! She will investigate long-term cognitive outcomes following COVID-19. Welcome, Katia!

Also, we are delighted that Marie Schweikard joins for her medical doctoral thesis. Marie is going to work with us on neuroimaging findings in patients with autoimmune encephalitis. Bienvenue, Marie!

We are also very happy to welcome Nina Stephan, who is joining in 2021 as a student assistant . Hello, Nina!

And last but not least, a warm welcome to Wei Zhao, who will join for his doctoral project in 2021. Hi, Wei!

Looking forward to working with you!

New members joining our lab!Nina2021-01-15T11:50:55+01:00

New review on cognitive dysfunction in autoimmune encephalitis

New review in Translational Psychiatry with colleagues from King’s College London – Cognitive impact of neuronal antibodies: encephalitis and beyond

The review describes the cognitive impairment associated with each antibody-mediated syndrome and discusses the potential role of autoantibodies on cognition.

Find the full publication here.

New review on cognitive dysfunction in autoimmune encephalitisNina2020-09-02T13:56:40+02:00

New paper in Annals of Neurology on clinical and MRI outcomes in pediatric NMDAR encephalitis

New paper in Annals of Neurology: Clinical and Magnetic Resonance Imaging Outcome Predictors in Pediatric Anti–N-Methyl-D-Aspartate Receptor Encephalitis

Longitudinal volumetric MRI analyses revealed significant brain volume loss and failure of age-expected brain growth in pediatric anti-NMDA receptor encephalitis. Abnormal MRI findings, a clinical presentation with sensorimotor deficits, and a treatment delay of over 4 weeks were identified as predictors of poor clinical outcome.

Find the full publication here.

New paper in Annals of Neurology on clinical and MRI outcomes in pediatric NMDAR encephalitischariteadmin2020-09-28T12:30:03+02:00

Preprint on dynamic FC in anti-NMDAR encephalitis

Preprint – State-dependent signatures of Anti-NMDA-Receptor Encephalitis

New preprint on temporal dynamics of functional connectivity in autoimmune encephalitis! State-wise group comparisons and supervised machine learning detect state-dependent alterations in patients that remain undetected in static analysis. Find the preprint here!

Preprint on dynamic FC in anti-NMDAR encephalitisNina2020-09-02T11:41:13+02:00

Amy Romanello joined the lab!

We are very glad to announce that Amy Romanello, currently writing her master’s thesis in our lab, will stay with us as a PhD student starting in October 2020. She was accepted for a full-time 3-year scholarship at the Berlin School of Mind and Brain to carry out her project, presently titled Temporal Complexity of Resting-State Brain Signals: Capturing the Dynamics of Spontaneous Brain Activity.

Amy Romanello joined the lab!Nina2020-08-24T11:19:54+02:00

Archiv and Ablage

[Written by Johanna on 2019/06/20]

The title will probably be the key word that appears in the wiki and is thus directly linked to your entry.

Table of content

What is it for?
- Ablage
- Archiv
How do I get access?
- Ablage
- Archiv
How do I store my data there?
- Ablage
- Archiv
Links

What is it for?

The Ablage and Archiv can be used to store your data. There are a few differences between the two:

Ablage

If you want to back-up data from a running project or want to save files/data your currently working with on a Charité-Server, you can use this folder. The Ablage has space for 8TB.

Archiv

Additionally to the Datenablage, we now have access to the Archiv (10TB). The Archiv can be used for data which won’t be modified anymore. Everybody should think about what they can put in the Archiv to save space in the Datenablage, e.g. already finished projects.

How do I get access?

Ablage

To store data in the Ablage, you need to get permission by the Charité IT.

You must fill out this form: https://intranet.charite.de/fileadmin/user_upload/microsites/gb/it/sys/Beantragung-Rechte.pdf

Johanna/Leonie can help you if you should have questions.

You then find the folder DATEN here:

(S:) CHARITE-DATEN-ABLAGE

– AG

-AG-Finke

-Daten

Archiv

Because we seriously cannot modify the data once it is uploaded in the Archiv, we have to be very careful what we put there. Everybody who got granted access to the Datenablage is also able to read the Archiv. However, only Maron and Johanna/Leonie have the possibility to upload data.

How do I store my data there?

Ablage

The folder structure is the following: \NAME\PROJECT

Please keep in mind that the space is limited to 8TB for the whole lab. To keep track of the Datenablage, Carsten made this google doc:

https://docs.google.com/spreadsheets/d/1a956pDa-BgsnxDtLHnEnZSvzaWu471Fp3_y3dLyh7tQ/edit#gid=0

Please put all the relevant information concerning the data you want to store in this spreadsheet.

Archiv

If you want to store data in the Archiv

(1) put your data in the folder ‘ready_for_archiv’ in the Datenablage

(2) Write a mail to Maron and/or Johanna/Leonie and we will move the data to the Archiv

Links

https://intranet.charite.de/fileadmin/user_upload/microsites/gb/it/sys/Beantragung-Rechte.pdf

Archiv and Ablagechariteadmin2020-04-01T10:24:30+02:00

Ethics

How to Ethics

Initially the most important task is to find out when the ethics committee meets, and then submit to them at least 14 days prior so that your application can be scheduled in for that meeting. Meeting dates for 2019 can be found here. The committee should generally get back to you within 10 days of the Meeting with a decision.

For your ethics submission you will require the following documents

Ethikantrag (Ethics Application)
Anschreiben (Cover Letter)
Studieninformation (Study Information for Participants),
Einwilligungserklärung (Participant Consent Form)
Case Report Form – in most cases this is not needed, but be sure to check first.

The Ethikantrag can be downloaded here. However, check on the website if there is a newer version.

The key to writing the Ethikantrag is to be clear and precise, but not too detailed. The latter may seem counter-intuitive, but being too specific in your explanations may then require you to submit amendments to ethics for every small change you want to make. Reviewers are unlikely to care about the specificities of your research, as their priority is ensuring that you have identified potential risks for participants and that participants are aware of their rights. Furthermore, in many cases, ethics is time-pressured and often submitted before you yourself have an extremely clear idea of the ins and outs of your study. An example of this would be saying “validated and commonly used tests of memory, attention and speed will be used to test the cognitive functioning of participants”, instead of listing out each and every test, and then later having to make an ethics amendment if you wish to change one. However, if you are already quite sure of what test you will be using, then by all means, list it.

There are many sections (e.g. data protection, insurance, participant rights) from each of the required documents which can be copied directly from previous submissions. Just ask a lab member if they could forward you one of the previous applications.

As for a general template or structure of the various required documents, Stephan kindly shared around approved Study Information and Consent forms for the V-Reha project in 2018 which can be found here.

Ethicschariteadmin2020-04-01T10:23:10+02:00

Github

HOW TO: GitHub for Version Control

[Written by Graham Cooper on 2019/15/01]

Table of content

Version Control in GitHub
Set up Git and GitHub
Git Commands
Links
Literature

Version Control in GitHub

Reproducibility ensures that anyone (including you in 6 months’ time!) can take your data and get the same results and tables that you originally found/generated. Problems with reproducibility (and how to overcome these) have been widely discussed in recent years, particularly in the behavioral sciences. One major obstacle standing in the way of reproducibility in research is good curation of data, i.e. storing everything in a sensible place, keeping track of changes in files by various collaborators. This is a particular challenge for us as researchers as (generally) we have been taught how to collect and analyze data to a high level of skill but have received next to no training in how to curate that data once it exists. Git (and GitHub) is one popular version control system that enables such data curation and is widely used in the field of software engineering, where the skills of data science/data management are taught to a gold standard. Using Git and GitHub, you have one space where all your relevant documents can be stored. Every version of your documents is saved so you can easily go back and check previous versions without needing to search through endless files names “manuscript_draft_version_16_FINAL_draft_ACTUAL_FINAL_DRAFT.doc”, for example! It also makes collaboration easier as everyone can work on the same document at once and merge versions, while keeping track of who did what. At the end of the project it also facilitates sharing of data and code as you can make a private repository public and add a link that everyone can access.

Currently GitHub allow users to have unlimited private repositories!

See Vuorre & Corley (2018) for a more detailed tutorial on Git and GitHub including how to set it up. A link to the online pdf is available in the links section.

Git Commands

Below is a list of common commands for Git and what they are used for.

git init

Initializes an empty git repository

git status

Shows all changes made since last “commit”

git add

Adds changes to the file to be committed

git commit -m “added file”

Commit all changes (signify that these changes should be included in the document). The text after the -m flag is the commit message that describes the changes you made

Links

Literature

Vuorre, M. & Curley, J. P. (2018) Curating Research Assets: A Tutorial on the Git Version Control System. Advances in Methods and Practices in Psychological Science, 1(2).

Githubchariteadmin2020-03-23T15:51:03+01:00