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pl-med2img

Abstract

pl-med2img is a ChRIS DS plugin that converts medical image data files (DICOM and NifTI) to web display-friendly formats (like png and jpg). This plug-in is a really a simple wrapper around the med2image application which is the actual workhorse converting NIfTI volumes or DICOM files to png or jpg formats. To better understand med2image and its features, please take a look at its repo: https://github.com/FNNDSC/med2image

Preconditions

This plugin requires input and output directories as a precondition.

How to pull medical image data

These medical image data files are in 2 formats: - NIfTI - DICOM

The following steps show how to pull sample files for NIfTI or DICOM files.

Pull NIfTI

The input should be a NIfTI volume with extension .nii.

We provide a sample volume here https://github.com/FNNDSC/SAG-anon-nii.git

  • Clone this repository (SAG-anon-nii) to your local computer.
git clone https://github.com/FNNDSC/SAG-anon-nii.git

Pull DICOM

The input should be a DICOM file usually with extension .dcm

We provide a sample directory of .dcm images here. (https://github.com/FNNDSC/SAG-anon.git)

  • Clone this repository (SAG-anon) to your local computer.
git clone https://github.com/FNNDSC/SAG-anon.git

Run

NOTE: Make sure that the 3 directories: pl-med2img, SAG-anon-nii, and SAG-anon are all within the same directory.

This plugin can be run in two modes:

  1. Natively as a python package
  2. As a containerized docker image.

Clone the git repository FNNDSC/pl-med2img in the current working directory (which also contains SAG-anon-nii and SAG-anon) using the following command

git clone https://github.com/FNNDSC/pl-med2img.git

Natively

Clone the repo and pip install the package

::
pip install -r requirements.txt pip install .

Make sure that your current working directory is the one that contains the 3 directories: pl-med2img, SAG-anon-nii, and SAG-anon

EXAMPLES:

NIFTI volume:

Create a directory called image-results-nii in the current working directory.

Run med2img using the following command to convert the NIfTI volume within the SAG-anon-nii directory to images:

med2img                                             \
    -i SAG-anon.nii                                 \
    -o sample.png                                   \
    ./SAG-anon-nii ./image-results-nii

DICOM files:

Create a directory called image-results-dcm in the current working directory.

Run med2img file using the following command to convert all DICOM files within the SAG-anon directory to images:

med2img                                                              \
    -i 0001-1.3.12.2.1107.5.2.19.45152.2013030808110258929186035.dcm \
    -o sample.png                                                    \
    ./SAG-anon ./image-results-DICOM

Using docker (preferred)

NOTE: Make sure that your current working directory is the one that contains the 3 directories: pl-med2img, SAG-anon-nii, and SAG-anon

First, pull the docker image using the following command:

docker pull fnndsc/pl-med2img .

Now, to run the docker image, see the following examples:

EXAMPLES:

NIFTI volume:

Run the docker image fnndsc/pl-med2img using the following command to convert the NIfTI files within the SAG-anon-nii directory to images:

docker run --rm                                         \
    -v $PWD/SAG-anon-nii/:/incoming                     \
    -v $PWD/image-results-nii/:/outgoing                \
    fnndsc/pl-med2img med2img                           \
    -i SAG-anon.nii                                     \
    -o sample.png                                       \
     /incoming /outgoing

DICOM files:

Run the docker image fnndsc/pl-med2img using the following command to convert the DICOM files within the SAG-anon directory to images:

docker run --rm                                                        \
    -v $PWD/SAG-anon/:/incoming                                        \
    -v $PWD/image-results-dcm/:/outgoing                               \
    fnndsc/pl-med2img med2img                                          \
    -i 0001-1.3.12.2.1107.5.2.19.45152.2013030808110258929186035.dcm   \
    -o sample.png                                                      \
     /incoming /outgoing

The above NIfTI or DICOM examples will push a copy of each file/folder in the container's /incoming storage. Some metadata files will be written to the container's /outgoing directory.

Make sure that the host $PWD/SAG-anon-nii or $PWD/SAG-anon directory is world readable and $PWD/image-results-nii or $PWD/image-results directory is world writable!

Development

To develop pl-med2img from within a containerized deployment, do

docker run --rm -it                                                     \
    -v $PWD/med2img:/usr/local/lib/python3.8/dist-packages/med2img:ro   \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw                    \
    fnndsc/pl-med2img med2img                                           \
    --inputFileSubStr "dcm" --sliceToConvert 0                          \
    /incoming /outgoing

(obviously in the above use whatever CLI flags are relevant to your debugging case).

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