dcm2niixpy package
Submodules
dcm2niixpy.dcm2niix module
- class DCM2NIIX(version, container_backend='singularity', download=False, download_folder=None)[source]
Bases:
object- __init__(version, container_backend='singularity', download=False, download_folder=None)[source]
Initialize the DCM2NIIX object.
- Parameters
container_backend (str, optional) – Either “docker” or “singularity”. Defaults to “singularity”.
version (str) – Docker tag of version to use. Defaults to None.
download (bool, optional) – Whether to download the container instead of pulling and running everytime. Defaults to False.
download_folder (str, optional) – Location to download the container to. Defaults to None.
- property container_backend: str
Get the container backend.
- Returns
Either “docker” or “singularity”.
- Return type
str
- property compression_level: int
gz compression level (1=fastest, 9=smallest).
Corresonds with ‘-1’ through ‘-9’ setting of dcm2niix.
- Returns
compression level. Defaults to 6
- Return type
int
- property adjacent_dicoms: bool
Whether all DICOMs are adjacent (images from same series are always in same folder).
Corresponds to ‘-a’ setting of dcm2niix.
- Returns
Whether all DICOMs are in same folder. Defaults to False
- Return type
bool
- property bids_sidecar: str
Whether to generate a bids sidecar.
y = yes, o = only bids sidecar, no nifti, n = no.
Corresponds to ‘-b’ setting of dcm2niix
- Returns
the bids sidecar setting. Defaults to y
- Return type
str
- property anonymize_bids_sidecar: str
Whether to anonymize the bids sidecar.
y = yes, n = no.
Corresponds to ‘-ba’ setting of dcm2niix.
- Returns
the bids sidecar anonymization setting. Defaults to y
- Return type
str
- property comments_in_aux: str
Whether to store comments in a NIfTI aux_file.
Provide up to 24 characters, e.g. first_visit.
Corresponds to ‘-c’ setting of dcm2niix
- Returns
the aux setting. No default
- Return type
str
- property directory_search_depth: str
Set the directory search depth.
Value can range from 0 to 9.
Corresponds to ‘-d’ setting of dcm2niix
- Returns
The directory search depth. Defaults to 5
- Return type
str
- property export_as_nrrd: str
Whether to save the file as NRRD instead of NIfTI.
y = yes, n = no.
Corresponds to ‘-e’ setting of dcm2niix.
- Returns
Whether to save as NRRD. Defaults to n.
- Return type
str
- property filename: str
The filename used to save the file.
The following parameters can be used and will be replaced in the string:
%a=antenna (coil) name
%b=basename
%c=comments
%d=description
%e=echo number
%f=folder name
%i=ID of patient
%j=seriesInstanceUID
%k=studyInstanceUID
%m=manufacturer
%n=name of patient
%o=mediaObjectInstanceUID
%p=protocol
%r=instance number
%s=series number
%t=time
%u=acquisition number
%v=vendor
%x=study ID
%z=sequence name
Corresponds to ‘-f’ setting of dcm2niix.
- Returns
The filename. Defaults to %f_%p_%t_%s
- Return type
str
- property generate_defaults: str
reset and write defaults; i=ignore: reset defaults], default n)
- Type
generate defaults file (y/n/o/i [o=only
- Return type
str
- property ignore_derived: str
ignore derived, localizer and 2D images (y/n, default n)
- Return type
str
- property losslessly_scale: str
losslessly scale 16-bit integers to use dynamic range (y/n/o [yes=scale, no=no, but uint16->int16, o=original], default n)
- Return type
str
- property merge_2d_slices: str
merge 2D slices from same series regardless of echo, exposure, etc. (n/y or 0/1/2, default 2) [no, yes, auto]
- Return type
str
- property convert_only_this_crc: str
only convert this series CRC number - can be used up to 16 times (default convert all)
- Return type
str
- property output_directory: None
output directory (omit to save to input folder)
- Return type
None
- property philips_precise_float_scaling: str
Philips precise float (not display) scaling (y/n, default y)
- Return type
str
- property rename: str
rename instead of convert DICOMs (y/n, default n)
- Return type
str
- property single_file_mode: str
single file mode, do not convert other images in folder (y/n, default n)
- Return type
str
- property private_text_notes: str
text notes includes private patient details (y/n, default n)
- Return type
str
- property verbose: str
verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic]
- Return type
str
- property conflict_write_behavior: str
0=skip duplicates, 1=overwrite, 2=add suffix)
- Type
write behavior for name conflicts (0,1,2, default 2
- Return type
str
- property crop_3D: str
crop 3D acquisitions (y/n/i, default n, use ‘i’gnore to neither crop nor rotate 3D acquistions)
- Return type
str
- property compress: str
- Return type
str
- property byte_order: str
- Return type
str
- property progress: str
- Return type
str
- property terse: str
- Return type
str