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=General information=
 
=General information=
  
−
==About Spinoza wiki==
+
==About the Spinoza wiki==
 
This site provides technical and procedural information for the Spinoza Centre community.  
 
This site provides technical and procedural information for the Spinoza Centre community.  
  
Line 12: Line 12:
 
==About the Spinoza Centre==
 
==About the Spinoza Centre==
  
−
The Spinoza Centre for Neuroimaging supports fundamental and clinical research programs in the fields of neuroscience and cognition but also facilitates academic and industrial research programs in areas other than the brain. The Centre houses a variety of techniques designed to visualize and study the brain. Central to the infrastructure are the 3 Tesla and 7 Tesla human Magnetic Resonance Imaging scanners (MRI). Ultra-high field MR (≥ 7 Tesla) allows human brain function, structure and metabolism to be visualized at unprecedented detail. The peripheral equipment installed at the scanners includes material for visual, auditory and sensory stimulation, eye tracking and electroencephalography (EEG) recordings, all of which can be performed simultaneously with the MRI acquisitions. Several testing rooms are available in the suite to help people who are collecting surveys, patient briefing or for obtaining behavioural and EEG measures. This allows for a wide range of possible experimental manipulation and physiological measurements to complement the MRI data. In addition to the MRI equipment the Spinoza Centre houses a 'mock' MRI scanner for training humans, and several groups share their setups for Transcranial Magnetic Stimulation (TMS) and Transcranial Direct Current Stimulation (tDCS) with the facility.
+
The Spinoza Centre for Neuroimaging supports fundamental and clinical research programs in the fields of neuroscience and cognition but also facilitates academic and industrial research programs in areas other than the brain. The Centre houses a variety of techniques designed to visualize and study the brain. Central to the infrastructure are the 3 Tesla and 7 Tesla human Magnetic Resonance Imaging scanners (MRI). Ultra-high field MRI (≥ 7 Tesla) allows human brain function, structure and metabolism to be visualized at unprecedented detail.  
 +
 
 +
The peripheral equipment installed at the scanners includes material for visual, auditory and sensory stimulation, eye tracking and electroencephalography (EEG) recordings, all of which can be performed simultaneously with the MRI acquisitions. Several testing rooms are available in the suite to help people who are collecting surveys, patient briefing or for obtaining behavioural and EEG measures. This allows for a wide range of possible experimental manipulation and physiological measurements to complement the MRI data.  
 +
 
 +
In addition to the MRI equipment the Spinoza Centre houses a 'mock' MRI scanner for training humans, and several groups share their setups for Transcranial Magnetic Stimulation (TMS) and Transcranial Direct Current Stimulation (tDCS) with the facility.
  
 
<div class="row">
 
<div class="row">
Line 20: Line 24:
 
   <p style="margin-left:10%>How to get to Spinoza via public transportation or car.</p>
 
   <p style="margin-left:10%>How to get to Spinoza via public transportation or car.</p>
  
−
   <p style="margin-left:5%><b>[[Opening hours]]</b></p>
+
   <p style="margin-left:5%><b>[[Opening hours]]*</b></p>
 
   <p style="margin-left:10%>Of Spinoza and when support staff are present.</p>
 
   <p style="margin-left:10%>Of Spinoza and when support staff are present.</p>
  
 
   <p style="margin-left:5%><b>[[Access to the building|How to get access]]</b></p>
 
   <p style="margin-left:5%><b>[[Access to the building|How to get access]]</b></p>
−
   <p style="margin-left:10%>To the building and facilities</p>
+
   <p style="margin-left:10%>How to get into the building and reach the facilities.</p>
  
 
   <p style="margin-left:5%><b>[[Available facilities|Available facilities]]</p>
 
   <p style="margin-left:5%><b>[[Available facilities|Available facilities]]</p>
−
   <p style="margin-left:10%>These include MRI scanners and peripheral equipment but also desks, internet, and meeting room. </p>
+
   <p style="margin-left:10%>These include research equipment but also desks, internet and meeting room. </p>
  
 
   <p style="margin-left:5%><b>[[House rules|User etiquette]]</b></p>
 
   <p style="margin-left:5%><b>[[House rules|User etiquette]]</b></p>
−
   <p style="margin-left:10%>Help us maintain a safe and productive environment for everyone</p>
+
   <p style="margin-left:10%>Please help us maintain a safe and productive environment for everyone.</p>
 +
 
 +
  <p style="margin-left:5%><b>[[Buttons and displays|Buttons and displays at SC]]*</b></p>
 +
  <p style="margin-left:10%>What is that button for?</p>
  
 
   </div>
 
   </div>
 
   <div class="large-6 columns">
 
   <div class="large-6 columns">
 
   <h2>Contact information</h2>
 
   <h2>Contact information</h2>
−
   <p style="margin-left:5%><b>[[Contact|Spinoza staff]]</b></p>
+
   <p style="margin-left:5%><b>[[Contact|Support & Contact]]</b></p>
−
   <p style="margin-left:10%>How to contact Spinoza staff.</p>
+
   <p style="margin-left:10%>Contact and support options</p>
  
 
   <p style="margin-left:5%><b>[[Mailing lists|General communication]]</b></p>
 
   <p style="margin-left:5%><b>[[Mailing lists|General communication]]</b></p>
Line 42: Line 49:
  
 
   <p style="margin-left:5%><b>[[SUM|Spinoza User Meetings]]</b></p>
 
   <p style="margin-left:5%><b>[[SUM|Spinoza User Meetings]]</b></p>
−
   <p style="margin-left:10%>Weekly presentations of staff, partners and other researchers.</p>
+
   <p style="margin-left:10%>Weekly presentations of staff, partners and other scientists about their research. Every Tuesday from 16:00-17:00, everyone is welcome!</p>
  
 
   <p style="margin-left:5%><b>[[Logos| Logos]]*</b></p>
 
   <p style="margin-left:5%><b>[[Logos| Logos]]*</b></p>
−
   <p style="margin-left:10%>Spinoza Centre Logos</p>
+
   <p style="margin-left:10%>Spinoza Centre Logos. Strictly speaking this has nothing to do with ''contact information'' but may be useful for some.</p>
 
   </div>
 
   </div>
 
</div>
 
</div>
Line 52: Line 59:
  
 
=Starting a new project=
 
=Starting a new project=
−
Below please find information if you would like to start a new MRI project at Spinoza. This information is primarily intended for researchers who are new to Spinoza.
+
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.
−
 
 
  
 
<div class="row">
 
<div class="row">
Line 59: Line 65:
 
   <h2>Starting to use the facilities</h2>
 
   <h2>Starting to use the facilities</h2>
 
   <p style="margin-left:5%><b>[[Starting a project|Compulsory actions]]</b></p>
 
   <p style="margin-left:5%><b>[[Starting a project|Compulsory actions]]</b></p>
−
   <p style="margin-left:10%>Checklist on how to start a project at Spinoza. These include compulsory actions ''far in advance'' and ''just prior to'' scanning.
+
   <p style="margin-left:10%>Checklist on how to start a project at Spinoza. These include compulsory actions that are required '''far in advance''' and '''just prior to''' scanning.
−
   </p>
+
   </p> 
−
  </div>
+
  <p style="margin-left:5%><b>[[Piloting|Piloting MRI projects]]</b></p>
 +
  <p style="margin-left:10%>About developing new protocols and trying out new things (and not necessarily getting billed <font size="+1">☺</font> ).</p>
 +
 
 +
</div>
 
   <div class="large-6 columns">
 
   <div class="large-6 columns">
 
   <h2>Training and safety</h2>
 
   <h2>Training and safety</h2>
 
   <p style="margin-left:5%><b>[[Certification for MR safety and MR operator|MR training and certification]]</b></p>
 
   <p style="margin-left:5%><b>[[Certification for MR safety and MR operator|MR training and certification]]</b></p>
−
   <p style="margin-left:10%>Prior to using the MR facilities please follow the MR safety training. Prior to scanning yourself you need to be trained as an MR operator. </p>
+
   <p style="margin-left:10%>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'''. </p>
  
−
   <p style="margin-left:5%><b>[[Training schedule|Safety training schedule]]</b></p>
+
   <p style="margin-left:5%><b>[[Training schedules|Safety training schedule]]*</b></p>
 
   <p style="margin-left:10%>Instructions on safety and evacuation training.</p>
 
   <p style="margin-left:10%>Instructions on safety and evacuation training.</p>
  
Line 73: Line 82:
 
   <p style="margin-left:10%>If you want to start already you may enlist help of those who are already trained.</p>
 
   <p style="margin-left:10%>If you want to start already you may enlist help of those who are already trained.</p>
  
−
   <p style="margin-left:5%><b>[[FerrAlert|Metal detectors]]</b></p>
+
   <p style="margin-left:5%><b>[[FerrAlert|Metal detectors]]*</b></p>
 
   <p style="margin-left:10%>How to use the metal detectors at Spinoza.</p>
 
   <p style="margin-left:10%>How to use the metal detectors at Spinoza.</p>
 
   </div>
 
   </div>
Line 87: Line 96:
 
   <h2>Participant procedures</h2>
 
   <h2>Participant procedures</h2>
 
   <p style="margin-left:5%><b>[[Sona|Participant recruitment (Sona)]]</b></p>
 
   <p style="margin-left:5%><b>[[Sona|Participant recruitment (Sona)]]</b></p>
−
   <p style="margin-left:10%>Researchers can make use of the Spinoza Sona participant registration system.</p>
+
   <p style="margin-left:10%>How to use of the Spinoza Sona participant registration system to recruit participants for your study.</p>
  
 
   <p style="margin-left:5%><b>[[Incidental findings| Incidental finding protocol]]*</b></p>
 
   <p style="margin-left:5%><b>[[Incidental findings| Incidental finding protocol]]*</b></p>
−
   <p style="margin-left:10%>Researchers can make use of our incidental finding protocol if also so specified in the ethical approval.</p>
+
   <p style="margin-left:10%>How to use our incidental finding protocol (if this was also so specified in your ethical approval).</p>
  
 
   <p style="margin-left:5%><b>[[Public data sharing]]*</b></p>
 
   <p style="margin-left:5%><b>[[Public data sharing]]*</b></p>
 
   <p style="margin-left:10%>Some notes on public data sharing which is part of the open science movement.</p>
 
   <p style="margin-left:10%>Some notes on public data sharing which is part of the open science movement.</p>
 +
 +
  <p style="margin-left:5%><b>[[Sharing data with participants]]*</b></p>
 +
  <p style="margin-left:10%>Some notes on how to deal with participants asking for their data.</p>
 +
 +
  <p style="margin-left:5%><b>[[Parking spot]]*</b></p>
 +
  <p style="margin-left:10%>How to book and use the Spinoza parking spot.</p>
  
 
   </div>
 
   </div>
 
   <div class="large-6 columns">
 
   <div class="large-6 columns">
 
   <h2>Basic MRI procedures</h2>   
 
   <h2>Basic MRI procedures</h2>   
−
   <p style="margin-left:5%><b>[[MRI costs and contacts for applying for partner hours|MRI costs ]]*</b></p>
+
   <p style="margin-left:5%><b>[[MRI costs|MRI costs ]]*</b></p>
−
   <p style="margin-left:10%>Hourly billing rate and contacts for applying for partner hours.</p>
+
   <p style="margin-left:10%>Hourly billing rate and contacts for applying for (free) partner hours.</p>
  
 
   <p style="margin-left:5%><b>[[Booking|Booking the scanner and cancellation policy]]</b></p>
 
   <p style="margin-left:5%><b>[[Booking|Booking the scanner and cancellation policy]]</b></p>
−
   <p style="margin-left:10%>Well... just that how to book and how to cancel scanner time.</p>
+
   <p style="margin-left:10%>Well... just that. How to book and how to cancel scanner time.</p>
 +
 
 +
  <p style="margin-left:5%><b>[[Best practices|Best practices]]*</b></p>
 +
  <p style="margin-left:10%>Set of guidelines for MRI data-analyses, strongly recommended by Spinoza staff.</p>
  
−
   <p style="margin-left:5%><b>[[Piloting|Piloting MRI projects]]</b></p>
+
   <p style="margin-left:5%><b>[[DataExport| Exporting PAR/REC data from the scanner]]*</b></p>
−
   <p style="margin-left:10%>Developing new protocols and trying out new things.</p>
+
   <p style="margin-left:10%>How to export your data from the scanner and send it to the server. </p>
  
−
   <p style="margin-left:5%><b>[[Data export| Data export and deletion policy]]</b></p>
+
   <p style="margin-left:5%><b>[[Naming_acquisitions | Conventions for consistent naming of your acquisitions]]*</b></p>
−
   <p style="margin-left:10%>How to get your data from the scanner.</p>
+
   <p style="margin-left:10%>How to name your acquisitions to facilitate automatic conversion and BIDS-ification.</p>
  
−
   <p style="margin-left:5%><b>[[FlyWheel| Flywheel platform]]</b></p>
+
   <p style="margin-left:5%><b>[[Data deletion policy| Data deletion policy]]*</b></p>
−
   <p style="margin-left:10%>Our new way of getting the data from the scanner and a variety of other things, including automatic QA and automatic preprocessing and allowing for data-sharing.</p>
+
   <p style="margin-left:10%>When data is deleted from the scanners.</p>
  
 
   <p style="margin-left:5%><b>[[Standard sequences @ 3T]]*</b></p>
 
   <p style="margin-left:5%><b>[[Standard sequences @ 3T]]*</b></p>
Line 117: Line 135:
 
   </div>
 
   </div>
 
</div>
 
</div>
−
----
+
 
  
 
----
 
----
  
 
= Advanced procedures and troubleshooting=  
 
= Advanced procedures and troubleshooting=  
−
Here we gather information for the adventurous MRI scientists using peripheral equipment and the most advanced procedures.  
+
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.
  
 
<div class="row">
 
<div class="row">
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   <p style="margin-left:5%><b>[[Electrical stimulator]]</b></p>
 
   <p style="margin-left:5%><b>[[Electrical stimulator]]</b></p>
−
   <p style="margin-left:10%>How to use the electrical stimulator in the scanner. (under development)</p>
+
   <p style="margin-left:10%>How to use the electrical stimulator in the scanner.</p>
  
 
   <p style="margin-left:5%><b>[[Physiology]]</b></p>
 
   <p style="margin-left:5%><b>[[Physiology]]</b></p>
−
   <p style="margin-left:10%>How to measure physiology in the scanner.</p>
+
   <p style="margin-left:10%>How to measure various physiological measures in the scanner, such as heart rate and respiration.</p>
 
   </div>
 
   </div>
 
   <div class="large-6 columns">
 
   <div class="large-6 columns">
 
   <h2>Advanced MRI procedures</h2>
 
   <h2>Advanced MRI procedures</h2>
 +
 +
  <p style="margin-left:5%><b>[[Common warnings and error messages]]*</b></p>
 +
  <p style="margin-left:10%>List of most common warnings and error messages both on 3T and 7T.</p>
  
 
   <p style="margin-left:5%><b>[[Patching 3T| Patching the 3T MRI scanners]]*</b></p>
 
   <p style="margin-left:5%><b>[[Patching 3T| Patching the 3T MRI scanners]]*</b></p>
−
   <p style="margin-left:10%>.</p>
+
   <p style="margin-left:10%>Well... just that. How to patch the 3T.</p>
  
−
   <p style="margin-left:5%><b>[[7Tdocs|7T MRI procedures and documentation]]*</b></p>
+
   <p style="margin-left:5%><b>[[7T_general_info_%26_troubleshooting|7T MRI procedures]]*</b></p>
−
   <p style="margin-left:10%>.</p>
+
   <p style="margin-left:10%>Documentation on 7T MRI procedures.</p>
 +
 
 +
  <p style="margin-left:5%><b>[[BOLD_hoist|Hoist the 7T BOLD screen]]*</b></p>
 +
  <p style="margin-left:10%>How to move the BOLD screen in the 7T setup.</p>
 +
 
 +
  <p style="margin-left:5%><b>[[7T_hardware|7T MRI Hardware]]*</b></p>
 +
  <p style="margin-left:10%>List of available coils on the 7T.</p>
 +
 
 +
  <p style="margin-left:5%><b>[[7T_phantoms|7T MRI Phantoms]]*</b></p>
 +
  <p style="margin-left:10%>List of available phantoms for the 7T.</p>
  
 
   <p style="margin-left:5%><b>[[7TQA|7T MRI Quality assurance]]*</b></p>
 
   <p style="margin-left:5%><b>[[7TQA|7T MRI Quality assurance]]*</b></p>
−
   <p style="margin-left:10%>.</p>
+
   <p style="margin-left:10%>How to run and evaluate the QA on the 7T.</p>
  
−
   <p style="margin-left:5%><b>[[Common warnings and error messages]]*</b></p>
+
   <p style="margin-left:5%><b>[[FAQS|FAQs on (f)MRI preprocessing]]*</b></p>
−
   <p style="margin-left:10%>.</p>
+
   <p style="margin-left:10%>BIDS, distortion correction, MP2RAGE(ME) etc.</p>
 +
 
 +
  <p style="margin-left:5%><b>[[Dicom send | Dicom transfer]]*</b></p>
 +
  <p style="margin-left:10%>How to send dicoms to the AMC from the Spinoza Linux cluster command line.</p>
  
−
  <p style="margin-left:5%><b></b></p>
 
−
  <p style="margin-left:10%>.</p>
 
 
   </div>
 
   </div>
 
</div>
 
</div>
 +
----

Revision as of 09:32, 18 July 2023


General information

About the Spinoza wiki

This site provides technical and procedural information for the Spinoza Centre community.

All users are invited to contribute their knowledge by editing content here. Obviously, it is important that you verify the accuracy of any information that you post.

Some parts of the wiki are only accessible by logging in (indicated with a "*"). You can login using your Spinoza account, if you don't have one please request the login information by sending an email to [email protected].

About the Spinoza Centre

The Spinoza Centre for Neuroimaging supports fundamental and clinical research programs in the fields of neuroscience and cognition but also facilitates academic and industrial research programs in areas other than the brain. The Centre houses a variety of techniques designed to visualize and study the brain. Central to the infrastructure are the 3 Tesla and 7 Tesla human Magnetic Resonance Imaging scanners (MRI). Ultra-high field MRI (≥ 7 Tesla) allows human brain function, structure and metabolism to be visualized at unprecedented detail.

The peripheral equipment installed at the scanners includes material for visual, auditory and sensory stimulation, eye tracking and electroencephalography (EEG) recordings, all of which can be performed simultaneously with the MRI acquisitions. Several testing rooms are available in the suite to help people who are collecting surveys, patient briefing or for obtaining behavioural and EEG measures. This allows for a wide range of possible experimental manipulation and physiological measurements to complement the MRI data.

In addition to the MRI equipment the Spinoza Centre houses a 'mock' MRI scanner for training humans, and several groups share their setups for Transcranial Magnetic Stimulation (TMS) and Transcranial Direct Current Stimulation (tDCS) with the facility.

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.

User etiquette

Please help us maintain a safe and productive environment for everyone.

Buttons and displays at SC*

What is that button for?

Contact information

Support & 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!

Logos*

Spinoza Centre Logos. Strictly speaking this has nothing to do with contact information but may be useful for some.

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 project 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 of the Spinoza Sona participant registration system to recruit participants for your study.

Incidental finding protocol*

How to use our incidental finding protocol (if this was also so specified in your ethical approval).

Public data sharing*

Some notes on public data sharing which is part of the open science movement.

Sharing data with participants*

Some notes on how to deal with participants asking for their data.

Parking spot*

How to book and use the Spinoza parking spot.

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 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 scanners*

Well... just that. How to patch the 3T.

7T MRI procedures*

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.

7T MRI Quality assurance*

How to run and evaluate the QA on 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.

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