MRI open source software tools enable automated processing of the magnetic resonance images of the human brain. These tools extract the inner and outer surfaces of the brain like cerebral cortex, segment and label sub region structures, and help to analyze imaging data. These tools also help to visualize and interact with the brain data. What are the open source tools for magnetic resonance images (MRI) ?
Hi, it depends on what kind of mri data you would like to analyse, and what exactly you need, e.g. image segmentation or diffuson weighted mri preprocessing and processing. Check out freesurfer (https://surfer.nmr.mgh.harvard.edu), itk-snap (http://www.itksnap.org/pmwiki/pmwiki.php), ants (http://stnava.github.io/ANTs/), afni (https://afni.nimh.nih.gov), fsl (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) or mrtrix3 (http://www.mrtrix.org).
Check Open fMRI for its wide variety of data:
https://openfmri.org/dataset/
Also:
http://mridata.org/list
Another great database:
http://fcon_1000.projects.nitrc.org/indi/IndiRetro.html
Check this too:
http://www.oasis-brains.org/#data
Hi, it depends on what kind of mri data you would like to analyse, and what exactly you need, e.g. image segmentation or diffuson weighted mri preprocessing and processing. Check out freesurfer (https://surfer.nmr.mgh.harvard.edu), itk-snap (http://www.itksnap.org/pmwiki/pmwiki.php), ants (http://stnava.github.io/ANTs/), afni (https://afni.nimh.nih.gov), fsl (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) or mrtrix3 (http://www.mrtrix.org).
Lucius has listed most of the common packages for MRI processing. I'd also add SPM (https://www.fil.ion.ucl.ac.uk/spm/) to that list as it too is very popular and convenient for those who prefer to use MATLAB. While MATLAB is itself not open source, the majority of the SPM code consists of standard MATLAB m-files that are open source.
For an exhaustive list of software applications for neuroimaging, check out the NeuroImaging Tools and Resources Collaboratory (NITRC) (https://www.nitrc.org/).
FreeSurfer, FSL, SPM, ANTS, MRtrix, ITK-SNAP etc are some of the more commonly used ones, but there are literally dozens of software packages specifically for MR image analysis. As stated above, it really depends upon what you want to do. Structural (e.g. T1w, T2w, diffusion), or functional (e.g. fMRI).
https://people.cas.sc.edu/rorden/dicom/index.html
https://en.wikipedia.org/wiki/List_of_neuroimaging_software
https://neuroscienceblueprint.nih.gov/resources-tools/neuroimaging-tools-and-resources-collaboratory-nitrc
It may also depend upon which operating system you are using (e.g. Windows, Linux, Mac). If you can be specific with what you specifically want to process, then appropriate open-source packages can be recommended.
In addition to the already mentioned tools I would also add the quite powerful Human Connectome Workbench: https://www.humanconnectome.org/software/connectome-workbench
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