The firstįilename hit that contains the will be assigned the Search of all the files in the using this flag.
Typically a DICOM file or a nifti volume.Īs a convenience, the input file can be determined via a substring Additional functions are planned for future releases. Which simply inverts the contrast intensity of the source image. Currently supported is -func invertIntensities Med2image also supports some very basic image processing through a -func CLI, which applies some canned transformation on the image. converting with -sliceToConvert -1 Special Operations NOTE: In case of DICOM images, the -reslice option will work only if all slices in the directory are converted, i.e.
No interpolation in the x and y directions is performed. Converted images are stored in subdirectories labeled x, y, and z. The z direction is the original acquistion (slice) direction, while x and y correspond to planes normal to the row and column directions. Since the script does not know the anatomical orientation of the image, the directions are simply labeled x, y, and z. However, by passing a -reslice to the script, all dimensions are converted. -d | -outputDir : The directory to contain the converted output image files.ĭicom-results/tags/anonymized-1449c1d-SAG_MPRAGE_220_FOV.jpg Multiple Direction Reslicingīy default, only the slice (or slices) in the acquisition direction are converted.This saves a user from needing to specify long and cumbersome file names, esp in the case of many DICOM filenames. By only specifying a sub string that identifies the file, the first file in the inputDir that contains the sub string is tagged as the inputFile. -inputFileSubStr : A short hand trick to specify the inputFile.Typically a DICOM file or a NifTI volume. -i | -inputFile : Input file to convert.Med2image needs at a minimum (some of) the following required command line arguments: The containerized version exposes a similar CLI and functionality as this module. We also offer a docker container of med2image as a ChRIS-conformant platform plugin here (see also the closely related that performs conversions down a directory tree recursively) - please that reference for information on running the dockerized container.
#CONVERT DICOM TO JPG PYTHON INSTALL#
Sudo apt-get install -y python3-tk Docker container One method of installing this script and all of its dependencies is by fetching it from PyPI. The script should work fine under Windows, but we have not actively tested on that platform - our dev envs are Linux Ubuntu and macOS. This document assumes UNIX conventions and a bash shell. matplotlib : (to save data in various image formats).pfmisc : (a general miscellaneous module for color support, etc).Make sure that the following dependencies are installed on your host system (or even better, a python3 virtual env): Med2image is a simple Python3 utility that converts medical image formatted files (such as DICOM and NifTI) to more web friendly ones, such as png and jpg.Ĭurrently, NIfTI and DICOM input formats are understood, while any graphical output type that is supported by matplotlib can be generated.Īt present med2image does not convert DICOM to NifTI, but this is planned for a future release. Convert DICOM or NIfTI inputs to jpg or png outputs.
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