├── .appveyor.yml ├── .codespellrc ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ ├── codespell.yml │ └── release.yml ├── .gitignore ├── .gitmodules ├── BATCH.md ├── BIDS ├── README.md └── extract_units.py ├── BidsGuess ├── BidsGuess.png └── README.md ├── CMakeLists.txt ├── COMPILE.md ├── CONTRIBUTE.md ├── Canon └── README.md ├── Dockerfile ├── ERRORS.md ├── FILENAMING.md ├── GE └── README.md ├── Mediso └── README.md ├── PARREC └── README.md ├── Philips └── README.md ├── README.md ├── RENAMING.md ├── Siemens └── README.md ├── SuperBuild ├── External-CLOUDFLARE-ZLIB.cmake ├── External-OPENJPEG.cmake ├── External-YAML-CPP.cmake └── SuperBuild.cmake ├── Troubleshooting └── README.md ├── UIH └── README.md ├── VERSIONS.md ├── batch_config.yml ├── cmake └── dcm2niixInitializeBuildType.cmake ├── console ├── CMakeLists.txt ├── Info.plist ├── base64.cpp ├── base64.h ├── cJSON.cpp ├── cJSON.h ├── charls │ ├── License.txt │ ├── README.md │ ├── charls.h │ ├── colortransform.h │ ├── constants.h │ ├── context.h │ ├── contextrunmode.h │ ├── decoderstrategy.h │ ├── defaulttraits.h │ ├── encoderstrategy.h │ ├── interface.cpp │ ├── jlscodecfactory.h │ ├── jpegimagedatasegment.h │ ├── jpegls.cpp │ ├── jpegmarkercode.h │ ├── jpegmarkersegment.cpp │ ├── jpegmarkersegment.h │ ├── jpegsegment.h │ ├── jpegstreamreader.cpp │ ├── jpegstreamreader.h │ ├── jpegstreamwriter.cpp │ ├── jpegstreamwriter.h │ ├── lookuptable.h │ ├── losslesstraits.h │ ├── processline.h │ ├── publictypes.h │ ├── scan.h │ └── util.h ├── dcm2niix_fswrapper.cpp ├── dcm2niix_fswrapper.h ├── jpg_0XC3.cpp ├── jpg_0XC3.h ├── main_console.cpp ├── main_console_batch.cpp ├── makefile ├── miniz.c ├── nifti1.h ├── nifti1_io_core.cpp ├── nifti1_io_core.h ├── nii_dicom.cpp ├── nii_dicom.h ├── nii_dicom_batch.cpp ├── nii_dicom_batch.h ├── nii_foreign.cpp ├── nii_foreign.h ├── nii_ortho.cpp ├── nii_ortho.h ├── notarize.sh ├── print.h ├── pypeline.log ├── tinydir.h ├── ucm.cmake ├── ujpeg.cpp ├── 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