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Introduction
============
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.
Dependencies
------------
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.
DcmStack requires the packages pydicom_ (>=0.9.7) and NiBabel_.
.. _pydicom: http://code.google.com/p/pydicom/
.. _nibabel: http://nipy.sourceforge.net/nibabel/
Installation
------------
Download the latest release from github_, and run easy_install on the
downloaded .zip file.
.. _github: https://github.com/moloney/dcmstack/tags
Basic Conversion
----------------
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*:
.. code-block:: console
$ 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 :doc:`CLI_Tutorial`.
Performing the conversion from Python code requires a few extra steps
but is also much more flexible:
.. code-block:: python
>>> import dcmstack
>>> from glob import glob
>>> src_dcms = glob('032-MPRAGEAXTI900Pre/*.dcm')
>>> stacks = dcmstack.parse_and_stack(src_dcms)
>>> stack = stacks.values[0]
>>> 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 :doc:`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.
.. code-block:: console
$ 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
:doc:`CLI_Tutorial`.
To work with the extended Nifti files from Python, use the *NiftiWrapper* class.
.. code-block:: python
>>> 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
:doc:`Python_Tutorial`.
For information on the DcmMeta extension see :doc:`DcmMeta_Extension`.
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