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  1. MRI: from DICOM to GLM Analysis
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  • Neurodesktop
  • MRI: from DICOM to GLM Analysis
    • 00 - Overview
    • 01 - DICOM to BIDS
    • 02 - Check IntendedFor field of the fmap’s JSON
    • 03 - T1w for PBn
    • 04 - Defacing
    • 05 - Removing Noise Scan
    • 06 - fMRIprep
    • 07 - Retinotopic Mapping
    • 08 - first level GLM
    • 09- second level GLM
    • Troubleshooting
  • MRI
    • MRI-Studies: General Information
    • 3D printing a brain
    • 7T anatomical analysis on neurodesk
    • MRI BIDS and OSF
    • fMRIprep analysis
    • MNI space
    • Old MRI setup
    • Update to the MRI lab setup
    • Physiological noise correction
  • Behavioral
    • Vision tests
    • BIDS for behavioral studies
    • Custom-built chin rests
  • People
    • Stipends and prizes for master and PhD students
    • Coffee time
    • Participant compensation
    • Things to do if you are leaving the lab
    • Scientific writing in practice
    • Research funding opportunities
  • Internship
    • Pflichtpraktikum
    • Internship Checklist
    • internship/claustrum_segmentation.qmd
  • Other Topics
    • Calculating a priori sample size using G Power
    • Gamma correction
    • Contribute to the website
    • Older ways to access the server
  • Labmeeting
  • Archive
Categories
All (11)
Analysis (5)
BIDS (1)
DICOM (1)
fmriPrep (4)
fMRIprep (1)
MRI (10)
Neurodesk (8)
nilearn (2)
Preprocessing (5)
Retinotopy (1)

MRI: from DICOMs to GLM

 
00 - Overview

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

MG
Jul 28, 2025
 
09- second level GLM
MRI
Analysis
fmriPrep
Neurodesk
nilearn

Example of second level GLM

MG
Jul 28, 2025

02 - Check IntendedFor field of the fmap’s JSON
MRI
Analysis
fmriPrep
Preprocessing
Neurodesk

Description of how to check and potentially update the fmap’s JSON file

MG
Jul 8, 2025
 
07 - Retinotopic Mapping
MRI
Retinotopy

Procedure to apply the probabilistic retinotopic mapping using the Benson Atlas

MG
May 5, 2025
 
08 - first level GLM
MRI
Analysis
fmriPrep
Neurodesk
nilearn

Several approaches to run a first level GLM using nilearn

MG
May 5, 2025

01 - DICOM to BIDS
MRI
DICOM
BIDS
Preprocessing
Neurodesk

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

MG
Apr 30, 2025

03 - T1w for PBn
MRI

Information about how to provide participants with their T1w image

MG
Apr 15, 2025

04 - Defacing
MRI
Preprocessing
Neurodesk

Step by step description of how to deface your data

MG
Apr 13, 2025

Troubleshooting
MRI
Analysis
fmriPrep
Preprocessing
Neurodesk

Collection of known potential problems and their solutions

MG
Mar 27, 2025

06 - fMRIprep
MRI
Analysis
fMRIprep
Neurodesk

Step by step description of how to run fMRIprep

MG
Mar 8, 2025

05 - Removing Noise Scan
MRI
Preprocessing
Neurodesk

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

MG
Mar 8, 2025
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