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
'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_dira pathlike object or string representing an existing directory

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

source_namesa 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.

anonymizea boolean

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

argsa string

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

collapse_foldersa boolean

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

config_filea pathlike object or string representing an existing file

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

convert_all_parsa boolean

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

date_in_filenamea boolean

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

environa 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_filenamea boolean

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

gzip_outputa boolean

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

id_in_filenamea boolean

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

nii_outputa boolean

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

output_dira 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_filenamea boolean

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

reorienta boolean

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

reorient_and_cropa boolean

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

source_in_filenamea boolean

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

spm_analyzea 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 0 -o ds005 -s n -v n dicomdir'
>>> converter.run()

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 0 -o ds005 -s n -v n .'
>>> converter.run()
source_dira 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_namesa 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_bidsa boolean

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

argsa string

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

bids_formata boolean

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

commenta 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)

compression1 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.

cropa boolean

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

environa 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_privatea boolean

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

ignore_deriva boolean

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

merge_imgs0 or 1 or 2

Merge 2D slices from same series regardless of echo, exposure, etc. - [0=no, 1=yes, 2=auto]. Maps to a command-line argument: -m %d. (Nipype default value: 0)

out_filenamea 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_dira pathlike object or string representing an existing directory

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

philips_floata boolean

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

series_numbersa list of items which are a string

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

single_filea boolean

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

to_nrrda boolean

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

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

property 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, search_crop)