nipype.interfaces.dcm2nii module

dcm2nii converts images from the proprietary scanner DICOM format to NIfTI.

Dcm2nii

Link to code

Bases: CommandLine

Wrapped executable: dcm2nii.

Uses MRIcron’s dcm2nii to convert dicom files

Examples

>>> from nipype.interfaces.dcm2nii import Dcm2nii
>>> converter = Dcm2nii()
>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.gzip_output = True
>>> converter.inputs.output_dir = '.'
>>> converter.cmdline  # doctest: +ELLIPSIS
'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'

source_dir : a pathlike object or string representing an existing directory

Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: source_names.

source_names : a list of items which are a pathlike object or string representing an existing file

Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: source_dir.

anonymize : a boolean

Remove identifying information. Maps to a command-line argument: -a. (Nipype default value: True)

args : a unicode string

Additional parameters to the command. Maps to a command-line argument: %s.

collapse_folders : a boolean

Collapse input folders. Maps to a command-line argument: -c. (Nipype default value: True)

config_file : a pathlike object or string representing an existing file

Load settings from specified inifile. Maps to a command-line argument: -b %s.

convert_all_pars : a boolean

Convert every image in directory. Maps to a command-line argument: -v. (Nipype default value: True)

date_in_filename : a boolean

Date in filename. Maps to a command-line argument: -d. (Nipype default value: True)

environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

events_in_filename : a boolean

Events (series/acq) in filename. Maps to a command-line argument: -e. (Nipype default value: True)

gzip_output : a boolean

Gzip output (.gz). Maps to a command-line argument: -g. (Nipype default value: False)

id_in_filename : a boolean

ID in filename. Maps to a command-line argument: -i. (Nipype default value: False)

nii_output : a boolean

Save as .nii - if no, create .hdr/.img pair. Maps to a command-line argument: -n. (Nipype default value: True)

output_dir : a pathlike object or string representing an existing directory

Output dir - if unspecified, source directory is used. Maps to a command-line argument: -o %s.

protocol_in_filename : a boolean

Protocol in filename. Maps to a command-line argument: -p. (Nipype default value: True)

reorient : a boolean

Reorient image to nearest orthogonal. Maps to a command-line argument: -r.

reorient_and_crop : a boolean

Reorient and crop 3D images. Maps to a command-line argument: -x. (Nipype default value: False)

source_in_filename : a boolean

Source filename. Maps to a command-line argument: -f. (Nipype default value: False)

spm_analyze : a boolean

SPM2/Analyze not SPM5/NIfTI. Maps to a command-line argument: -s. Mutually exclusive with inputs: nii_output.

bvals : a list of items which are a pathlike object or string representing an existing file bvecs : a list of items which are a pathlike object or string representing an existing file converted_files : a list of items which are a pathlike object or string representing an existing file reoriented_and_cropped_files : a list of items which are a pathlike object or string representing an existing file reoriented_files : a list of items which are a pathlike object or string representing an existing file

Dcm2niix

Link to code

Bases: CommandLine

Wrapped executable: dcm2niix.

Uses Chris Rorden’s dcm2niix to convert dicom files

Examples

>>> from nipype.interfaces.dcm2nii import Dcm2niix
>>> converter = Dcm2niix()
>>> converter.inputs.source_dir = 'dicomdir'
>>> converter.inputs.compression = 5
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir'
>>> converter.run() # doctest: +SKIP

In the example below, we note that the current version of dcm2niix converts any files in the directory containing the files in the list. We also do not support nested filenames with this option. Thus all files must have a common root directory.

>>> converter = Dcm2niix()
>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.compression = 5
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n .'
>>> converter.run() # doctest: +SKIP

source_dir : a pathlike object or string representing an existing directory

A directory containing dicom files to be converted. Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: source_names.

source_names : a list of items which are a pathlike object or string representing an existing file

A set of filenames to be converted. Note that the current version (1.0.20180328) of dcm2niix converts any files in the directory. To only convert specific files they should be in an isolated directory. Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: source_dir.

anon_bids : a boolean

Anonymize BIDS. Maps to a command-line argument: -ba. Requires inputs: bids_format.

args : a unicode string

Additional parameters to the command. Maps to a command-line argument: %s.

bids_format : a boolean

Create a BIDS sidecar file. Maps to a command-line argument: -b. (Nipype default value: True)

comment : a unicode string

Comment stored as NIfTI aux_file. Maps to a command-line argument: -c %s.

compress : ‘y’ or ‘i’ or ‘n’ or ‘3’

Gzip compress images - [y=pigz, i=internal, n=no, 3=no,3D]. Maps to a command-line argument: -z %s. (Nipype default value: y)

compression : 1 or 2 or 3 or 4 or 5 or 6 or 7 or 8 or 9

Gz compression level (1=fastest, 9=smallest). Maps to a command-line argument: -%d.

crop : a boolean

Crop 3D T1 acquisitions. Maps to a command-line argument: -x. (Nipype default value: False)

environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

has_private : a boolean

Text notes including private patient details. Maps to a command-line argument: -t. (Nipype default value: False)

ignore_deriv : a boolean

Ignore derived, localizer and 2D images. Maps to a command-line argument: -i.

merge_imgs : a boolean

Merge 2D slices from same series. Maps to a command-line argument: -m. (Nipype default value: False)

out_filename : a unicode string

Output filename template (%a=antenna (coil) number, %c=comments, %d=description, %e=echo number, %f=folder name, %i=ID of patient, %j=seriesInstanceUID, %k=studyInstanceUID, %m=manufacturer, %n=name of patient, %p=protocol, %s=series number, %t=time, %u=acquisition number, %v=vendor, %x=study ID; %z=sequence name). Maps to a command-line argument: -f %s.

output_dir : a pathlike object or string representing an existing directory

Output directory. Maps to a command-line argument: -o %s. (Nipype default value: .)

philips_float : a boolean

Philips precise float (not display) scaling. Maps to a command-line argument: -p.

series_numbers : a list of items which are a unicode string

Selectively convert by series number - can be used up to 16 times. Maps to a command-line argument: -n %s....

single_file : a boolean

Single file mode. Maps to a command-line argument: -s. (Nipype default value: False)

to_nrrd : a boolean

Export as NRRD instead of NIfTI. Maps to a command-line argument: -e.

verbose : a boolean

Verbose output. Maps to a command-line argument: -v. (Nipype default value: False)

bids : a list of items which are a pathlike object or string representing an existing file bvals : a list of items which are a pathlike object or string representing an existing file bvecs : a list of items which are a pathlike object or string representing an existing file converted_files : a list of items which are a pathlike object or string representing an existing file

Dcm2niix.version

interfaces should implement a version property

class nipype.interfaces.dcm2nii.Info

Bases: nipype.interfaces.base.core.PackageInfo

Handle dcm2niix version information

static parse_version(raw_info)

version_cmd = 'dcm2niix'

nipype.interfaces.dcm2nii.search_files(prefix, outtypes)