med2image 1.1.2

快速概述

• 将DICOM或NIFTI转换为JPG或PNG

概述

med2image是一个简单的python3实用程序，用于转换医学图像 格式化后的文件，如png和jpg。

目前，nifti和dicom的输入格式是可以理解的，而任何 可以生成matplotlib支持的图形输出类型。

依赖关系

确保在主机上安装了以下依赖项 系统/Python3虚拟环境：

• nibabel（读取nifti文件）
• pydicom（读取dicom文件）
• matplotlib（以各种图像格式保存数据）
• 枕头（以JPG格式保存数据）

pip3 install med2image

sudo apt-get update
sudo apt-get install -y python3-tk

命令行参数

-i|--inputFile <inputFile>
Input file to convert. Typically a DICOM file or a nifti volume.

[-d|--outputDir <outputDir>]
The directory to contain the converted output image files.

-o|--outputFileStem <outputFileStem>
The output file stem to store conversion. If this is specified
with an extension, this extension will be used to specify the
output file type.

SPECIAL CASES:
For DICOM data, the <outputFileStem> can be set to the value of
an internal DICOM tag. The tag is specified by preceding the tag
name with a percent character '%', so

    -o %ProtocolName

will use the DICOM 'ProtocolName' to name the output file. Note
that special characters (like spaces) in the DICOM value are
replaced by underscores '_'.

Multiple tags can be specified, for example

    -o %PatientName%PatientID%ProtocolName

and the output filename will have each DICOM tag string as
specified in order, connected with dashes.

A special %inputFile is available to specify the input file that
was read (without extension).

[-t|--outputFileType <outputFileType>]
The output file type. If different to <outputFileStem> extension,
will override extension in favour of <outputFileType>.

[-s|--sliceToConvert <sliceToConvert>]
In the case of volume files, the slice (z) index to convert. Ignored
for 2D input data. If a '-1' is sent, then convert *all* the slices.
If an 'm' is specified, only convert the middle slice in an input
volume.

[-f|--frameToConvert <sliceToConvert>]
In the case of 4D volume files, the volume (V) containing the
slice (z) index to convert. Ignored for 3D input data. If a '-1' is
sent, then convert *all* the frames. If an 'm' is specified, only
convert the middle frame in the 4D input stack.

[--showSlices]
If specified, render/show image slices as they are created.

[--reslice]
For 3D data only. Assuming [i,j,k] coordinates, the default is to save
along the 'k' direction. By passing a --reslice image data in the 'i' and
'j' directions are also saved. Furthermore, the <outputDir> is subdivided into
'slice' (k), 'row' (i), and 'col' (j) subdirectories.

[-x|--man]
Show full help.

[-y|--synopsis]
Show brief help.

nifti转换

理解3d和4d nifti输入数据。对于4D Nifti， 特定的帧可以与特定的切片一起指定 索引。在大多数情况下，只需要一个切片，因为大多数nifti数据是 而且，所有的切片都可以转换，或者只转换中间的切片。

med2image --inputFile vol.nii     --outputDir out      \
          --outputFileStem image  --outputFileType jpg \
          --sliceToConvert -1

image-slice000.jpg
image-slice001.jpg
image-slice002.jpg
image-slice003.jpg
image-slice004.jpg
image-slice005.jpg
image-slice006.jpg
image-slice007.jpg
...
image-slice049.jpg
image-slice050.jpg
image-slice051.jpg
image-slice052.jpg
image-slice053.jpg

DICOM转换

多方向重新标记

默认情况下，只有采集方向上的切片 转换。但是，通过向脚本传递-r，所有维度都是 转换。因为剧本不知道 图像和方向简单地标记为X、Y和Z。

Z方向是原始采集（切片）方向，而X方向 y对应于垂直于行和列方向的平面。

转换后的图像存储在标有X、Y和Z的子目录中。