MRI

05 fmriprep

Step by step description of how to run fmriprep

00 - from DICOM to GLM

Overview about how to get from DICOM files from the Scanner to your GLM Analysis

04 - Removing Noise Scan

Step by step description of how to remove the denoising scan from your data

03 - Defacing

Step by step description of how to deface your data

01 DICOM to BIDS

Step by step description of how to get from DICOM files to necessary nifti-files in BIDS format

02 T1w for PBn

Information about how to provide participants with their T1w image

Troubleshooting

Collection of known potential problems and their solutions

Old MRI setup

Information about running experiments in the MRI lab (before the new computer arrived!)

Update to the MRI lab setup

The MRI lab has had some upgrades in 2024 including:

Neurodesktop access

How to use Neurodesktop on the server

Dicom to Bids conversion

how to convert from dicom’s to bids

FreeSurfer FSFAST

Information about running an FSFAST analysis on Neurodesk

fMRIprep analysis

Information about using fMRIprep to preprocess fMRI data

7T anatomical analysis on neurodesk

How to run 7 Tesla anatomy analysis on neurodesk

MRI BIDS and OSF

Information about BIDS and OSF

Physiological noise correction

Creating physiology regressors using the PhysIO toolbox

3D printing a brain

current procedure for 3d printing brains