Software tools

These are just a few external resources we find interesting. We don’t own them, can’t promise they’ll always work, and all credit goes to the original creators—please check their sites for details.

General

• 3D Slicer: https://www.slicer.org/
• AFNI: https://afni.nimh.nih.gov/
• BIDS: https://bids.neuroimaging.io/index.html
• BrainVoyager: https://www.brainvoyager.com/
• CARET: https://www.nitrc.org/projects/caret/
• CONN: https://web.conn-toolbox.org/
• Freesurfer: https://surfer.nmr.mgh.harvard.edu/
• FSL: https://fsl.fmrib.ox.ac.uk/fsl/docs/#/
• Mevislab: https://www.mevislab.de/de/
• MRIcron: https://www.nitrc.org/projects/mricron
• MRIcrogl:https://www.nitrc.org/projects/mricrogl/
• MRIqc: https://mriqc.readthedocs.io/en/latest/
• SPM: https://www.fil.ion.ucl.ac.uk/spm/software/

Anatomy

• CAT12: https://neuro-jena.github.io/cat12-help/#intro

ASL

• ASL prep: https://aslprep.readthedocs.io/en/latest/
• Explore ASL: https://sites.google.com/view/exploreasl

DTI/DWI

• Explore DTI: https://www.exploredti.com/
• KULeuven – Fun With Tracts: https://github.com/KUL-Radneuron/KUL_FWT
• MRtrix: https://www.mrtrix.org/

fMRI

• fMRIprep: https://fmriprep.org/en/stable/

MRS

• FSL MRS: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/
• Gannet: https://www.gabamrs.com/gannet
• jMRUI: http://www.jmrui.eu/
• LC Model: https://www.win.ox.ac.uk/research/it/i-want-to/research-area/mrs/lcmodel
• MRS Hub https://mrshub.org/software_all/
• Osprey: https://www.gabamrs.com/osprey