The dcmstack software allows series of DICOM images to be stacked into multi-dimensional arrays. These arrays can be written out as Nifti files with an optional header extension (the DcmMeta extension) containing a summary of all the meta data from the source DICOM files.
Either Python 2.6 or 2.7 is required. With Python 2.6 it is not possible to maintain the order of meta data keys when reading back the JSON.
Download the latest release from github, and run easy_install on the downloaded .zip file.
The software consists of the python package (dcmstack) with two command line interfaces (dcmstack and nitool).
It is recommended that you sort your DICOM data into directories (at least per study, but perferably by series) before conversion.
To convert directories of DICOM data from the command line you generally just need to pass the directories to dcmstack:
$ dcmstack -v 032-MPRAGEAXTI900Pre/ Processing source directory 032-MPRAGEAXTI900Pre/ Found 64 source files in the directory Created 1 stacks of DICOM images Writing out stack to path 032-MPRAGEAXTI900Pre/032-MPRAGE_AX_TI900_Pre.nii.gz
Here we use the verbose flab (-v) to show what is going on behind the scenes. To embed the DcmMeta header extension we need to use the –embed option. For more information see CLI Tutorial.
Performing the conversion from Python code requires a few extra steps but is also much more flexible:
>>> import dcmstack >>> from glob import glob >>> src_dcms = glob('032-MPRAGEAXTI900Pre/*.dcm') >>> stacks = dcmstack.parse_and_stack(src_dcms) >>> stack = stacks.values >>> nii = stack.to_nifti() >>> nii.to_filename('output.nii.gz')
The parse_and_stack function has many optional arguments that closely match the command line options for dcmstack. To embed the DcmMeta extension pass embed_meta=True to the to_nifti method. For more information see Python Tutorial.
Basic Meta Data Usage¶
To work with Nifti files containing the embedded DcmMeta extension on the command line, use the nitool command. The nitool command has several sub commands.
$ nitool lookup InversionTime 032-MPRAGE_AX_TI900_Pre.nii.gz 900.0
Here we use the lookup sub command to lookup up the value for ‘InversionTime’. For more information about using nitool see CLI Tutorial.
To work with the extended Nifti files from Python, use the NiftiWrapper class.
>>> from dcmstack import dcmmeta >>> nii_wrp = dcmmeta.NiftiWrapper.from_filename('032-MPRAGE_AX_TI900_Pre.nii.gz') >>> nii_wrp.get_meta('InversionTime') 900.0
For more information on using the NiftiWrapper class see Python Tutorial.
For information on the DcmMeta extension see DcmMeta Extension.