kaggie/mripy

Consolidation of MRI or Medical Imaging Code

mripy

Consolidation of MRI Databases (AWESOME MRI! -- for google)

Welcome to the mripy wiki!

0D MRI

OpenSource MRI

• Openmri.github.io/ocra
• https://github.com/opencore Opencore nmr
• https://github.com/mtwieg/NMR/ Mtwieg github.com
• http://od1n.sourceforge.net/ medusa Stanford
• http://www.opensourceimaging.org/project/gr-mri-a-software-package-for-magnetic-resonance-imaging-using-software-defined-radios/
• https://imr-framework.github.io/ (Pulseq) OCRA

MEG

• https://github.com/mne-tools/mne-hcp

Vendor Specific Support

• https://spinsights.chem.agilent.com/login.jspa?referer=%252Findex.jspa
• https://collaborate.mr.gehealthcare.com/
• https://www.mr-idea.com/
• https://www.bruker.com/service/information-communication/nmr-pulse-program-lib/bruker-user-library.html

1D MRI

Spectroscopy

• https://scion.duhs.duke.edu/vespa/gamma
• https://github.com/chenkonturek/MRS_MRI_libs
• https://github.com/openmrslab/suspect
• https://github.com/SIVICLab/sivic
• https://github.com/cni/MRS
• https://github.com/jjhelmus/nmrglue
• https://github.com/LarsonLab/hyperpolarized-mri-toolbox
• http://hugadams.github.io/scikit-spectra/

Pulse design

• https://github.com/ekgibbons/slr/blob/master/python/slr.py
• https://github.com/LarsonLab/Spectral-Spatial-RF-Pulse-Design
• https://scion.duhs.duke.edu/vespa/

Bloch Equations

• https://github.com/bretglun/BlochBuster
• https://github.com/leoliuf/MRiLab
• https://github.com/neji49/bloch-simulator-python
• https://github.com/k7hoven/blochsimu
• https://github.com/mriesch-tum/mbsolve
• https://pypi.org/project/blochsimu/
• http://qutip.org/download.html
• http://www.drcmr.dk/bloch
• https://github.com/jtamir/mri-sim-py/blob/master/epg/epg.py

Pulse Sequence Design

• https://github.com/pulseq/pulseq
• https://github.com/magland/sequencetree5
• https://pulseq.github.io/
• https://toppemri.github.io/
• http://www.jemris.org/ug_command_line.html
• https://github.com/wgrissom/ISMRM-RF-Pulse-Design-Challenge

SPGR

• https://github.com/mezera/mrQ

Bruker

• https://github.com/tesch1/BruKitchen
• https://github.com/jdoepfert/brukerMRI
• https://github.com/cmwalker/Bruker
• https://github.com/jamesjcook/mat_recon_pipe
• https://github.com/bennomeier/pyNMR

2D and 3D MRI

Image reconstruction

• https://github.com/mrirecon/bart
• https://github.com/gadgetron/gadgetron-python-ismrmrd-client
• https://github.com/ismrmrd/ismrmrd-python
• https://github.com/mikgroup/espirit-python

Offline / Adjacent Recon

• https//yarra.rocks
• https://github.com/gadgetron/gadgetron

Non-Uniform FFT

• https://github.com/dfm/python-nufft
• https://github.com/jakevdp/nufftpy
• https://github.com/cea-cosmic/pysap

Registration

• https://pypi.org/project/imreg_dft/
• https://simpleelastix.github.io/
• https://fsl.fmrib.ox.ac.uk/fsl/fslwiki

Neuroimaging in Python

• https://github.com/swederik/nipype
• http://nipype.readthedocs.io/en/latest/devel/software_using_nipype.html

Susceptibility Mapping

• https://github.com/lruthotto/QSMReconstruction.m
• https://github.com/sunhongfu/QSM
• https://github.com/mathieuboudreau/qsm-tools
• https://github.com/daiweis05/QITK
• https://github.com/philgd/CVI-MRI

Compressed Sensing

• https://github.com/topics/compressed-sensing
• https://github.com/thomaskuestner/CS_MoCo_LAB
• https://mrfil.github.io/PowerGrid

Spin echo

• https://github.com/jyhmiinlin/cineFSE

• https://github.com/jtamir/mri-sim-py/blob/master/epg/epg.py

• http://mrsrl.stanford.edu/~brian/bloch/

• https://www.ismrm.org/MR-Hub/

Other

• https://github.com/sammba-mri/sammba-mri
• https://bitbucket.org/norok2/pymrt/

4D MRI

T1 and T2 Mapping

• https://github.com/gattia/PyMap
• https://github.com/gdurin/pyFitting
• https://github.com/neuropoly/qMRLab

DCE

• https://github.com/welcheb/pydcemri

Diffusion

• https://github.com/flohorovicic/pynoddy
• https://github.com/ecaruyer/qspace
• https://github.com/jsjol/NOW
• https://diffusionmritool.github.io/tutorial_qspacesampling.html
• https://github.com/nipy/dipy
• https://github.com/AthenaEPI/dmipy
• https://www.nitrc.org/projects/noddi_toolbox
• https://github.com/cbclab/MDT
• https://github.com/NYU-DiffusionMRI/Diffusion-Kurtosis-Imaging
• https://github.com/DiffusionMRITool/dmritool-MultiShellSampling
• https://bitbucket.org/siawoosh/acid-artefact-correction-in-diffusion-mri/

CEST Sources

• https://github.com/cest-sources/BM_sim_fit

fMRI and pupil size analysis

• https://github.com/tknapen/FIRDeconvolution

Intracranial electrodes in MRI

• https://github.com/kingjr/ecoggui

ND MRI

T1 T2 Shuffling

• https://github.com/jtamir/t2shuffling-support

MR Fingerprinting

• https://github.com/welcheb/Hamburg_MRF_workshop_VUMC_results

• https://github.com/peng-cao/mripy

• https://www.ismrm.org/mri_unbound/sequence.htm

• https://bitbucket.org/asslaender/nyu_mrf_recon

• https://github.com/Corey-Zumar/MRI-Reconstruction

• https://github.com/StephanZheng/neural-fingerprinting

Connectome

• https://www.nitrc.org/projects/cviewer/
• https://github.com/dPys/PyNets

Biobank

• https://oai.epi-ucsf.org/datarelease/
• http://www.ukbiobank.ac.uk/
• http://cai2r.net/resources/software/one-hundred-knee-mri-cases

Radiomics

• https://github.com/Radiomics/pyradiomics
• https://github.com/Radiomics/SlicerRadiomics
• https://pypi.org/project/MedPy/
• https://github.com/QTIM-Lab/DeepNeuro

Knee

• https://bitbucket.org/marcniethammer/ksrt/wiki/Home

NI Learn for Brain Mapping

• https://github.com/nilearn/nilearn
• https://github.com/WinawerLab
• https://github.com/mwaskom/lyman
• https://github.com/jlohmeier/atlasBREX
• https://github.com/taigw/brats17

Machine learning

• https://github.com/js3611/Deep-MRI-Reconstruction
• https://github.com/Kamnitsask/deepmedic
• Github.com/FlorianKnoll
• Colah.github.io/post/2015-08-Backprop
• https://qtim-lab.github.io/research/

General Machine Learning (not MRI)

• https://github.com/KaimingHe/deep-residual-networks
• https://github.com/ry/tensorflow-resnet
• https://github.com/pytorch/vision/blob/master/torchvision/models/resnet.py
• https://github.com/DeepLearnPhysics/pytorch-resnet-example
• https://github.com/alexjc/neural-enhance
• https://github.com/david-gpu/srez
• https://github.com/mriphysics
• https://github.com/khcs/brain-synthesis-lesion-segmentation/blob/master/utils/merge_2d_test_to_nii.py
• https://github.com/ad12/DOSMA

Radiofrequency and Electromagnetism

FDTD

• https://github.com/stevengj/meep

FDFD

• http://www.mit.edu/~wsshin/maxwellfdfd.html

Finite Element

• http://sfepy.org/doc-devel/index.html
• https://github.com/AppliedMechanics-EAFIT/SolidsPy

RF Coils

• https://github.com/neuropoly/coil_simulation_web
• https://github.com/BIC-MNI/mrisim
• https://github.com/leoliuf/MRiLab
• https://github.com/usc-mrel/lowfieldsim
• https://github.com/adamkettinger/phase-optimization-for-VCC
• https://github.com/thanospol/MARIE
• https://bitbucket.org/wgrissom/gnuradio-mri/src/master/

Gradient Coils

• https://github.com/gBringout/CoilDesign

Mesh Extraction

• https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-mri/browse/mri2mesh

Other Modalities

Xray

• https://github.com/pydata/xarray

Other (part a.0.0.0.0.0.0.1)

https://web.eecs.umich.edu/~fessler/code/ BART http://gpilab.com/ http://mridata.org/

Other (part a.0.0.0.0.0.0.2)

http://people.eecs.berkeley.edu/~mlustig/Software.html

https://gitlab.com/mariadeprez/irtk-public

https://github.com/khammernik

Tools to think about

Check out Gitlab.com, Github.com, Bitbucket.com, Docker, Jupyter, Binder, BART, MIRT, PowerGrid, GPI