The software used by IRMage team
This page regroups the software frequently used by the IRMaGe team to process MRI data.
If you would like help or feedback about those software in order to processe your data acquired on the IRMaGe scanner, please do not hesitate to contact your IRMaGe contact.
This list is not exhaustive. If you are planning to analyse your data acquired on the IRMaGe scanner with a software not in this list and you would like some feedback from IRMaGe, please get in touch with your contact at IRMaGe. A member of IRMaGe team may be familiar with this software and will help you get startded.
| Software suite | |
|---|---|
| POPULSE MIA | https://populse.github.io/populse_mia |
| BrainVisa | https://brainvisa.info |
| Nipype | https://nipype.readthedocs.io |
| Data conversion | |
| mri_conv | https://populse.github.io/mri_conv |
| dcm2bids | https://unfmontreal.github.io/Dcm2Bids/3.1.1/ |
| Quality control | |
| MRIQC | https://mriqc.readthedocs.io/ |
| Structural MRI (sMRI) | |
| SPM | https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/vbm/ |
| VolBrain Assemblynet | https://github.com/volBrain/AssemblyNet |
| Diffusion MRI (dMRI) | |
| MRTrix | https://mrtrix.readthedocs.io |
| QSIPrep | https://qsiprep.readthedocs.io |
| dipy* | https://docs.dipy.org/1.8.0/ |
| FSL DTIFIT | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT |
| TractSeg | https://github.com/MIC-DKFZ/TractSeg |
| AFQ | https://yeatmanlab.github.io/pyAFQ/ |
| AMICO | https://github.com/daducci/AMICO |
| Functional MRI (fMRI) | |
| SPM | https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/fmri/ |
| fMRIPrep | https://fmriprep.org/ |
| nilearn* | https://nilearn.github.io |
| Spectroscopy | |
| Gannet* | https://github.com/richardedden/gannet3.1 |
| ASL | |
| ExploreASL | https://exploreasl.github.io |
| Quantitative MRI | |
| hMRI toolbox | https://hmri-group.github.io |
*basic knowledge