Package: quantiphyse
QuantiphyseViewer and data processing for 3D/4D medical imaging dataOverviewQuantiphyse provides tools for modelling and analysis of 3D/4D volumetric data, principally MRI data.Core features:Loading/Saving 3D/4D NIFTI filesAnalysis tools including single/multiple voxel analysis and data comparisonGeneric processing including smoothing, resampling, clusteringFeatures available via pluginsRegistration, motion correctionModelling tools for DCE, ASL, DSC and CEST MRIIntegration of selected FSL toolsSee:http://quantiphyse.readthedocs.org/en/latest/for full documentation.LicenseQuantiphyse is available free under an academic (non-commercial) license. See theLICENSEfile for
full details, and contactOUIif interested in
commercial licensing.InstallationSeehttps://quantiphyse.readthedocs.io/en/latest/basics/install.htmlfor current installation
instructionsRunning from source code (for developers)Running from source is recommended only if your are interested in developing the software further.Install the dependencies:The list of Python dependencies is inrequirements.txtFor example:pip install -r requirements.txtBuild extensionspython setup.py build_ext --inplaceRun from source directorypython qp.pyPackagingThe scripts packaging/build.py is used to build a frozen distribution package in the form of a compressed archive (tar.gzor.zip)
and a platform-dependent package (deb,msiordpg). It should run autonomously, however you may need to input the sudo password
on Linux in order to build adebpackage.The--snapshotoption removes the version number from package filenames so you can provided them for download without having to change the link URLs.The--maxioption builds a package which includes selected plugins, assuming these are downloadedTo Do listIssue trackerCurrent issues can be viewed on the GitHub issue tracker (https://github.com/physimals/quantiphyse/issues)Roadmapv0.6 (Released June 2018)ASL tools first version (preprocess, model fit, calibration, multiphase)Improved viewer (full resolution, aligned)v0.8 (Target Mar 2019)Integration of selected FSL tools (FLIRT, FAST, BET, FSL_ANAT?)      [x]Improved registration support (apply transform)                      [x]Improved ASL tools based on oxasl (inc. ENABLE, VEASL, DEBLUR)       [x]Fabber T1                                                            [x]Fabber DCE                                                           [x]DSC widget                                                           [x]Improvements to ROI builder - working 'paint' tool                   [x]Motion simulation                                                    [x]Add noise                                                            [x]v0.10 (Target 2020)Stable interface for QpWidget, QpData, Process                       [ ]Python 3                                                             [x]Support PySide and PySide2 - ideally the latter by default           [x]Improved manual data alignment tools                                 [ ]Multi-overlay view                                                   [x]Perfusion simulator                                                  [x]Migration to PySide2Current version of Quantipihyse is targeted at Pyside2Shouldstill run under Pyside1 but not guaranteedCurrently using our own fork ofpyqtgraphawaiting official release with Pyside2 supportVague Plans for FutureMoCo/RegistrationBartek's MC method3D viewProbably not that useful but fun and may be easy(?) with vispy. Reliant on good refactoring of ImageViewApplication to surfaces (Tom K?)Use VisPy?Add Jola's texture analysis which sounds cool, whatever it isPK modelling validationQIBA [x]QINSimplify/rewrite generic Fabber interfaceImprove memory usage by swapping out data which are not being displayed?All widgets which process within ROI should work with the subimage within the bounding box of the
ROI, not the whole image.Supervoxels does this already with great performance improvement.Support other file formats using NIBABEL.DICOM conversion included where DCMSTACK is availableAdd semiquantitative measuresArea under the curveEnhancing fraction