Centre for Imaging Research (CIR)

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Centre for Imaging Research (CIR)

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NatMEG
NatMEG
- Preparation
  Preparation
- SQUID Acquisition
  SQUID Acquisition
- OPM Acquisition
  OPM Acquisition
- Stimulus Equipment
  Stimulus Equipment
  - Audio
    Audio
    
    Audio mixer
    
    Audiofile
    
    B&K sound level meter and artificial ear
    
    Behringer specs
    
    Soundtubes specs
    
    Speakers specs
  - Visual
    Visual
    
    Screen and projector
    
    Showing visual stimuli on the screen
  - Other
    Other
    
    ENS specs
    
    Mechanical pain specs
    
    Olfaction specs
    
    Pleasant touch specs
    
    Tactile specs
- Response Equipment
  Response Equipment
- Presentation
  Presentation
  - Presentation
  - Presentation script tips
  - Examples
    Examples
    
    Auditory oddball paradigm
    
    Resting state paradigm example
- Preprocessing
  Preprocessing
  - Using the GUI
  - Pipeline
  - About MaxFilter
    
    About MaxFilter
- Other
  Other
- MEEG-analyis
  MEEG-analyis
  - Tips and tricks
    
    Tips and tricks
    
    Tips for writing useful analysis scripts
    
    Consistent filenames in loops
    
    Estimate rank
    
    How to find all raw files that belongs to the same condition
    
    Ignore split trials between fif files
    
    Loop through figures for inspection
    
    MATLAB paths
    
    Morphing, normalization, and transforming source spaces and coordinate systems (MNE)
    
    Plot head-channel alignment in FieldTrip
    
    Read non MaxFiltered data
    
    Read split files into FieldTrip
    
    Select a limited number of trials in FieldTrip
- NatMEG server (legacy)
  NatMEG server (legacy)
  - Set-up connection
    Set-up connection
    
    Connect to Archive
    
    Connect to Storage
    
    Connect to Compute
    
    Close VNC connection
  - Install software
    Install software
    
    Freesurfer
    
    R and RStudio
    
    Set up Anaconda and mamba
    
    FieldTrip
    
    MNE-Python
  - Script tips
    
    Script tips
  - Troubleshooting
    Troubleshooting
    
    Alt-key does not work from vncserver window
    
    Connection error - pop-op asking for authentification for update
    
    MNE coregistration crash
    
    MNE errors when plotting
    
    PyQt5.QtWebKitWidgets error in Spyder
    
    R/Rstudio trouble shooting
    
    SFTP (or samba) not working
    
    Scrambled MEG sensor locations
    
    Terminal does not open
    
    Errors with trigger channel STI016 in Neuromag data
    
    Undefined function 'fiff_read_epochs'
    
    VNC black screen error
    
    rstanarm install problem
- Cerberos
  Cerberos
BMIC
BMIC
- Getting Started
  Getting Started
  - Mounting Network Drives
  - Setting up Flexiview
- Solena
  Solena
  - Initial Setup
  - Using Solena
- BIDS at BMIC
  BIDS at BMIC
MRC
MRC
- BIDS at MRC
- 3T CIR Protocol
- Response Equipment
  Response Equipment
  - Eye-tracker
SPICE
SPICE
- How to connect
- Best practices for using SPICE
- Tips for using VScode
- Download your data
- BIDS
- Software
  Software
  - Anaconda
  - FSL
  - FreeSurfer
  - Matlab
  - R
- Singularity containers
  Singularity containers
  - fMRIPrep
  - Heudiconv
  - Halfpipe
  - MRIQC

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