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MRIQC
Alexander Holmes edited this page Jul 5, 2023
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MRIQC: Quality control software for multimodal MRI data - the source code is written in Python but run in bash
Requires BIDS organised data
We’ve developed an adapted QC pipeline that includes MRIQC’s image quality metrics (IQMs) with scripts on kg98
- ~/kg98/aholmes/freesurfer_holmesQC
- 0.0 NSB Programming Courses (in ALPHA)
- 1.0 Working on the Cluster
- 2.0 Programming Languages
- 2.1 Python
- 2.1.1 Getting Set Up
- 2.1.2 Coding in Python
- 2.1.3 Applications of Python in Neuroimaging
- 2.2 MATLAB
- 2.3 R and RStudio
- 2.4 Programming Intro Exercises
- 2.5 git and GitHub
- 2.6 SLURM and Job Submission
- 2.1 Python
- 3.0 Neuroimaging Tools and Packages
- 3.1 BIDS
- 3.2 FreeSurfer
- 3.3 FSL
- 3.4 Connectome Workbench/wb_command
- 3.5 fMRIPrep
- 3.6 QSIPrep
- 3.7 MICApipe
- 3.8 MRIQC
- 4.0 Specialist Tools