¶ General information
¶ About the Spinoza wiki
This wiki provides technical and procedural information for the Spinoza Centre community. All members of the Spinoza community are invited to contribute their knowledge by editing content here.
Some parts of are only accessible by logging in using your Spinoza account (indicated with a "*"). If you don't have a Spinoza account please request one by sending an email to info@spinozacentre.nl.
¶ About the Spinoza Centre
To understand the human brain, we have to measure it. Spinoza houses the most powerful MRI machine in Amsterdam region.
The Spinoza Centre for Neuroimaging supports fundamental and clinical research in neuroscience and cognition, while also facilitating academic and industrial research beyond brain studies. The Spinoza Center provides advanced imaging techniques, with 3T and 7T MRI scanners at its core. Ultra-high field MRI (≥7T) provides unparalleled detail in visualizing human brain function, structure, and metabolism.
The scanners are equipped with tools for visual, auditory, and sensory stimulation, eye tracking, and EEG recordings, all compatible with MRI. Dedicated testing rooms support surveys, patient briefings, and behavioral or EEG assessments, enabling diverse experimental manipulations and physiological measurements to complement MRI data. The Spinoza Centre also features a mock MRI scanner for training and shared setups for Transcranial Magnetic Stimulation (TMS) and Transcranial Direct Current Stimulation (tDCS).
¶ The facilities
- Route description
How to get to Spinoza via public transportation or car. - Opening hours*
Of Spinoza and when support staff are present. - How to get access
How to get into the building and reach the facilities. - Available facilities
These include research equipment but also desks, internet and meeting room. - House rules and user etiquette
Please help us maintain a safe and productive environment for everyone.
¶ Contact information
- Support and contact
Contact and support options - General communication
How to join general communication lists of Spinoza. - Spinoza User Meetings
Weekly presentations of staff, partners and other scientists about their research.
Every Tuesday from 16:00 - 17:00, everyone is welcome!
¶ Starting a new project
Below please find the information you need, if you would like to start a new MRI project at Spinoza. This information is primarily intended for researchers who are new to Spinoza. You typically only have to go through these procedures once.
¶ Starting to use the facilities
- Compulsory actions
Checklist on how to start a projct at Spinoza. These include compulsory actions that are required far in advance and just prior to scanning. - Piloting MRI projects
About developing new protocols and trying out new things (and not necessarily getting billed
).
¶ Training and safety
- MR training and certification
Prior to using the MR facilities please follow the MR safety training. If you want perform the scanning yourself, you need to be trained as an MR operator. - Safety training schedule*
Instructions on safety and evacuation training. - List of certified users*
If you want to start already you may enlist help of those who are already trained. - Metal detectors*
How to use the metal detectors at Spinoza.
¶ Basic procedures
Below please find the basic procedures most MRI scientists will encounter sooner or later during their project.
¶ Participant procedures
- Participant recruitment (Sona)
How to use the Spinoza Sona participant registration system to recruit participants for your study. - Incidental finding protocol
What to do if you think you found something abnormal in your participant's data. - Parking spot for participants with mobility problems*
How to book and use the dedicated Spinoza parking spot close to the Spinoza entrance. - Data sharing*
Some notes on public data sharing as part of open science, but also how to deal with participants asking for their data.
¶ Basic MRI procedures
- MRI costs*
Hourly billing rate and contacts for applying for (free) partner hours. - Booking the scanner and cancellation policy
Well... just that. How to book and how to cancel scanner time. - Best practices*
Set of guidelines for MRI data-analyses, strongly recommended by Spinoza staff. - Exporting PAR/REC data from the scanner*
How to export your data from the scanner and send it to the server. - Conventions for consistent naming of your acquisitions*
How to name your acquisitions to facilitate automatic conversion and BIDS-ification. - Data deletion policy*
When data is deleted from the scanners. - Standard sequences @ 3T*
Tried and tested sequences easily adaptable to your needs.
¶ Advanced procedures and troubleshooting
Here we gather information for the adventurous MRI scientist using peripheral equipment and the most advanced procedures. This section also contains usage and troubleshooting information for the MRI scientists and MR operators.
¶ Peripheral MRI equipment
- Stimulus computer
How to control your stimulus from outside the scanner. - MRI compatible LCD screen (BOLDscreen)
How to use the screen in the scanner. - MRI compatible button boxes (FORP)
How to use the response buttons in the scanner. - MRI compatible audio system (MRconfon)
How to use the audio setup in the scanner. - MRI compatible eye trackers
How to track the participants eye-movements in the scanner. - Auxilliary EMG, ECG and GSR recordings (BrainAmp)
How to record EMG, ECG and GSR in the scanner. (under development) - EEG-fMRI recordings (EGI)
How to record EEG in the scanner. - Electrical stimulator
How to use the electrical stimulator in the scanner. - Physiology
How to measure various physiological measures in the scanner, such as heart rate and respiration.
¶ Advanced MRI procedures
- Common warnings and error messages*
List of most common warnings and error messages both on 3T and 7T. - Patching the 3T MRI scanner*
Well... just that. How to patch the 3T. - 7T MRI procedures
Documentation on 7T MRI procedures. - 7T MRI procedures_new*
Documentation on 7T MRI procedures. - Hoist the 7T BOLD screen*
How to move the BOLD screen in the 7T setup. - 7T MRI hardware*
List of available coils on the 7T. - 7T MRI phantoms*
List of available phantoms for the 7T. - FAQs on (f)MRI preprocessing*
BIDS, distortion correction, MP2RAGE(ME) etc. - DICOM transfer
How to send DICOMS to the AMC from the Spinoza Linux cluster command line.
¶ Internal
- Staff pages*
Procedures for Spinoza staff members