nifti2dicom

reconstruct DICOM files given one NIfTI and two DICOM files

Dependencies

1. Python 3.x
2. NumPy

   NumPy is the fundamental package for scientific computing with Python.

   pip3 install numpy
   

3. NiBabel

   Read / write access to some common neuroimaging file formats.

   pip3 install nibabel
   

4. Pydicom

   Pydicom is a pure Python package for working with DICOM files such as medical images, reports, and radiotherapy objects.

   pip3 install pydicom
   

5. (recommended) Unidecode

   ASCII transliterations of Unicode text.

   pip3 install unidecode
   

Usage

dicom2nifti

Split directory by series in case DICOM files belong to different series (files are copied).

Then, convert each set of DICOM files to a NIfTI file.

./dicom2nifti.py PATH [-o]

positional arguments:

1. PATH directory of DICOM files

optional arguments:

• -o, --orient orient output NIFTI file

Each series must contain at least two DICOM files.

nifti2dicom

Convert each NIfTI file in a directory to a set of DICOM files.

./nifti2dicom.py PATH

positional arguments:

1. PATH directory of NIfTI files or path of a NIfTI file

At least two DICOM files must be present in the directory of the NIfTI files.

In case path holds the path of a NIfTI file, only that NIfTI file will be taken into account.

nifti2dicom2

./nifti2dicom2.py PATH

Convert NIfTI files to DICOM.

positional arguments:

1. PATH directory of NIfTI files or path of a NIfTI file

A set of DICOM files is located in PATH. Then, for each NIfTI file in PATH, a subdirectory is created with a copy of the DICOM. Pixel Data (0x7fe0, 0x0010) in every copy of the original DICOM set is replaced by image data of the corresponding NIfTI file. The Data Set Trailing Padding (0xfffc, 0xfffc) tag is ignored. In case PATH holds the path of a NIfTI file, only that NIfTI file is taken under consideration, while the DICOM files set is located in the directory of the NIFTI file.

Tools

dicomtools-dataset

Output the dataset of a DICOM file.

./dicomtools.py dataset PATH

positional arguments:

1. PATH path to the NIfTI file

Pixel Data (0x7fe0, 0x0010) and Data Set Trailing Padding (0xfffc, 0xfffc) tags are ignored.

dicomsplit

Place each DICOM file in a subdirectory according to Protocol Name and Series Number.

./dicomsplit.py PATH [-m] [-f] [-v]

positional arguments:

1. PATH directory of mixed DICOM files

optional arguments:

• -m, --move move files instead of copying
• -f, --force overwrite existing subdirectories
• -s, --single run even if all DICOM files belong to the same series
• -v, --verbose print actions

dicomtable

Output a table with the variable fields of a DICOM set as a CSV.

./dicomtable.py PATH

positional arguments:

1. PATH directory of DICOM files

dicomdiff

Print the difference of the headers between two DICOM files.

./dicomdiff.py dcm1 dcm2

dicomcmp

Compare data of all corresponding DICOM files in two directories.

./dicomcmp.py dir1 dir2 [-v]

optional arguments:

• -v, --verbose print the result of each comparison

return values:

• 0 on success
• 1 on failure

niftitools-header

Output the header of a NIfTI file.

./niftitools.py header PATH

positional arguments:

1. PATH path to the NIfTI file

niftitools-affine

Output the affine of a NIfTI file.

./niftitools.py affine PATH

positional arguments:

1. PATH path to the NIfTI file

niftitools-orient

Orient a NIfTI file.

./niftitools.py orient INPATH [-o OUTPATH] [-d]

positional arguments:

1. INPATH path to the input NIfTI file

optional arguments:

• -o OUTPATH, --outpath OUTPATH path to the output NIfTI file; default INPATH-oriented
• -d, --diagonal apply orientation only if resulting affine is close to diagonal

niftidiff

Print the difference of the headers between two NIfTI files.

./niftidiff.py nii1 nii2

nifticmp

Compare data of two NIfTI files.

./nifticmp.py nii1 nii2

return values:

• 0 on success
• 1 on failure

References

• Defining the DICOM orientation
• Siemens mosaic format
• Siemens format DICOM with CSA header
• The NIFTI file format
• NIfTI conversion, visualization and transformation tools