DICOM Tags in the NIfTI Header¶
NIfTI images include an extended header (see the NIfTI Extensions Standard)
to store, amongst others, DICOM tags and attributes. When NiBabel loads a NIfTI
file containing DICOM information (a NIfTI extension with ecode == 2), it
parses it and returns a pydicom dataset as the content of the NIfTI extension.
This can be read and written to in order to facilitate communication with
software that uses specific DICOM codes found in the NIfTI header.
For example, the commercial PMOD software stores the Frame Start and Duration times of images using the DICOM tags (0055, 1001) and (0055, 1004). Here’s an example of an image created in PMOD with those stored times accessed through nibabel.
>> import nibabel as nib
>> nim = nib.load('pmod_pet.nii')
>> dcmext = nim.header.extensions[0]
>> dcmext
Nifti1Extension('dicom', '(0054, 1001) Units CS: 'Bq/ml'
(0055, 0010) Private Creator LO: 'PMOD_1'
(0055, 1001) [Frame Start Times Vector] FD: [0.0, 30.0, 60.0, ..., 13720.0, 14320.0]
(0055, 1004) [Frame Durations (ms) Vector] FD: [30000.0, 30000.0, 30000.0,600000.0, 600000.0]'))
Tag |
Name |
Value |
|---|---|---|
(0054, 1001) |
Units |
CS: ‘Bq/ml’ |
(0055, 0010) |
Private Creator |
LO: ‘PMOD_1’ |
(0055, 1001) |
[Frame Start Times Vector] |
FD: [0.0, 30.0, 60.0, …, 13720.0, 14320.0 |
(0055, 1004) |
[Frame Durations (ms) Vector] |
FD: [30000.0, 30000.0, 30000.0, …, 600000.0, 600000.0 |
Access each value as you would with pydicom:
>> ds = dcmext.get_content()
>> start_times = ds[0x0055, 0x1001].value
>> durations = ds[0x0055, 0x1004].value
Creating a PMOD-compatible header is just as easy:
>> nim = nib.load('pet.nii')
>> nim.header.extensions
[]
>> from dicom.dataset import Dataset
>> ds = Dataset()
>> ds.add_new((0x0054,0x1001),'CS','Bq/ml')
>> ds.add_new((0x0055,0x0010),'LO','PMOD_1')
>> ds.add_new((0x0055,0x1001),'FD',[0.,30.,60.,13720.,14320.])
>> ds.add_new((0x0055,0x1004),'FD',[30000.,30000.,30000.,600000.,600000.])
>> dcmext = nib.nifti1.Nifti1DicomExtension(2,ds) # Use DICOM ecode 2
>> nim.header.extensions.append(dcmext)
>> nib.save(nim,'pet_withdcm.nii')
Be careful! Many imaging tools don’t maintain information in the extended header, so it’s possible [likely] that this information may be lost during routine use. You’ll have to keep track, and re-write the information if required.
Optional Dependency Note: If pydicom is not installed, nibabel uses a generic
nibabel.nifti1.Nifti1Extension header instead of parsing DICOM data.