fsl.data.dicom
¶
This module provides the DicomImage
class, which represents a
volumetric DICOM data series. The DicomImage
is simply an `Image
which provides accessors for additional DICOM meta data.
The following other functions are provided in this module, which are thin
wrappers around functionality provided by Chris Rorden’s dcm2niix
program:
Returns |
|
Uses the |
|
Takes a DICOM series meta data dictionary, as returned by |
See: https://github.com/rordenlab/dcm2niix/
Note
These functions will not work if an executable called dcm2niix
cannot be found.
- fsl.data.dicom.MIN_DCM2NIIX_VERSION = (1, 0, 2017, 12, 15)¶
Minimum version of
dcm2niix
that is required for this module to work.
- fsl.data.dicom.CRC_DCM2NIIX_VERSION = (1, 0, 2019, 9, 2)¶
For versions of
dcm2niix
orf this version or newer, the-n
flag, used to convert a single DICOM series, requires that a CRC checksum identifying the series be passed (see theseriesCRC()
function). Versions prior to this require the series number to be passed.
- class fsl.data.dicom.DicomImage(*args, **kwargs)[source]¶
Bases:
fsl.data.image.Image
The
DicomImage
is a volumetricImage
with some associated DICOM metadata.The
Image
class is used to manage the data and the voxel-to-world transformation. Additional DICOM metadata may be accessed via theImage
metadata access methods.- __init__(image, metadata, dicomDir, *args, **kwargs)[source]¶
Create a
DicomImage
.- Parameters
image – Passed through to
Image.__init__()
.metadata – Dictionary containing DICOM meta-data.
dicomDir – Directory that the dicom image was loaded from.
- property dicomDir¶
Returns the directory that the DICOM image data was loaded from.
- __annotations__ = {}¶
- __module__ = 'fsl.data.dicom'¶
- fsl.data.dicom.compareVersions(v1, v2)[source]¶
Compares two
dcm2niix
versionsv1
andv2
. The versions are assumed to be in the format returned byinstalledVersion()
.- Returns
1 if
v1
is newer thanv2
-1 if
v1
is older thanv2
0 if
v1
the same asv2
.
- fsl.data.dicom.enabled()[source]¶
Returns
True
ifdcm2niix
is present, and recent enough,False
otherwise.
- fsl.data.dicom.scanDir(dcmdir)[source]¶
Uses the
dcm2niix -b o
option to generate a BIDS sidecar JSON file for each series in the given DICOM directory. Reads them all in, and returns them as a sequence of dicts.- Some additional metadata is added to each dictionary:
DicomDir
: The absolute path todcmdir
- Parameters
dcmdir – Directory containing DICOM series
- Returns
A list of dicts, each containing the BIDS sidecar JSON metadata for one DICOM series.
- fsl.data.dicom.seriesCRC(series)[source]¶
Calculate a checksum string of the given DICOM series.
The returned string is of the form:
SeriesCRC[.echonumber]
Where
SeriesCRC
is an unsigned integer which is the CRC32 checksum of theSeriesInstanceUID
, andechonumber
is theEchoNumber
of the series - this is only present for multi-echo data, where the series is from the second or subsequent echos.- Parameters
series – Dict containing BIDS metadata about a DICOM series, as returned by
scanDir()
.- Returns
String containing a CRC32 checksum for the series.
- fsl.data.dicom.loadSeries(series)[source]¶
Takes a DICOM series meta data dictionary, as returned by
scanDir()
, and loads the associated data as one or more NIFTI images.- Parameters
series – Dictionary as returned by
scanDir()
, containing meta data about one DICOM data series.- Returns
List containing one or more
DicomImage
objects.