interfaces.dcm2nii

Dcm2nii

Link to code

Wraps command 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'

Inputs:

[Mandatory]
source_dir: (an existing directory name)
        flag: %s, position: -1
        mutually_exclusive: source_names
source_names: (a list of items which are an existing file name)
        flag: %s, position: -1
        mutually_exclusive: source_dir

[Optional]
anonymize: (a boolean, nipype default value: True)
        Remove identifying information
        flag: -a
args: (a unicode string)
        Additional parameters to the command
        flag: %s
collapse_folders: (a boolean, nipype default value: True)
        Collapse input folders
        flag: -c
config_file: (an existing file name)
        Load settings from specified inifile
        flag: -b %s
convert_all_pars: (a boolean, nipype default value: True)
        Convert every image in directory
        flag: -v
date_in_filename: (a boolean, nipype default value: True)
        Date in filename
        flag: -d
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', nipype default value: {})
        Environment variables
events_in_filename: (a boolean, nipype default value: True)
        Events (series/acq) in filename
        flag: -e
gzip_output: (a boolean, nipype default value: False)
        Gzip output (.gz)
        flag: -g
id_in_filename: (a boolean, nipype default value: False)
        ID in filename
        flag: -i
nii_output: (a boolean, nipype default value: True)
        Save as .nii - if no, create .hdr/.img pair
        flag: -n
output_dir: (an existing directory name)
        Output dir - if unspecified, source directory is used
        flag: -o %s
protocol_in_filename: (a boolean, nipype default value: True)
        Protocol in filename
        flag: -p
reorient: (a boolean)
        Reorient image to nearest orthogonal
        flag: -r
reorient_and_crop: (a boolean, nipype default value: False)
        Reorient and crop 3D images
        flag: -x
source_in_filename: (a boolean, nipype default value: False)
        Source filename
        flag: -f
spm_analyze: (a boolean)
        SPM2/Analyze not SPM5/NIfTI
        flag: -s
        mutually_exclusive: nii_output

Outputs:

bvals: (a list of items which are an existing file name)
bvecs: (a list of items which are an existing file name)
converted_files: (a list of items which are an existing file name)
reoriented_and_cropped_files: (a list of items which are an existing
         file name)
reoriented_files: (a list of items which are an existing file name)

Dcm2niix

Link to code

Wraps command 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 # should 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

Inputs:

[Mandatory]
source_dir: (an existing directory name)
        A directory containing dicom files to be converted
        flag: %s, position: -1
        mutually_exclusive: source_names
source_names: (a list of items which are an existing file name)
        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
        flag: %s, position: -1
        mutually_exclusive: source_dir

[Optional]
anon_bids: (a boolean)
        Anonymize BIDS
        flag: -ba
        requires: bids_format
args: (a unicode string)
        Additional parameters to the command
        flag: %s
bids_format: (a boolean, nipype default value: True)
        Create a BIDS sidecar file
        flag: -b
comment: (a unicode string)
        Comment stored as NIfTI aux_file
        flag: -c %s
compress: ('y' or 'i' or 'n' or '3', nipype default value: y)
        Gzip compress images - [y=pigz, i=internal, n=no, 3=no,3D]
        flag: -z %s
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)
        flag: -%d
crop: (a boolean, nipype default value: False)
        Crop 3D T1 acquisitions
        flag: -x
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', nipype default value: {})
        Environment variables
has_private: (a boolean, nipype default value: False)
        Flag if text notes include private patient details
        flag: -t
ignore_deriv: (a boolean)
        Ignore derived, localizer and 2D images
        flag: -i
merge_imgs: (a boolean, nipype default value: False)
        merge 2D slices from same series
        flag: -m
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)
        flag: -f %s
output_dir: (an existing directory name, nipype default value: .)
        Output directory
        flag: -o %s
philips_float: (a boolean)
        Philips precise float (not display) scaling
        flag: -p
series_numbers: (a list of items which are a unicode string)
        Selectively convert by series number - can be used up to 16 times
        flag: -n %s...
single_file: (a boolean, nipype default value: False)
        Single file mode
        flag: -s
verbose: (a boolean, nipype default value: False)
        Verbose output
        flag: -v

Outputs:

bids: (a list of items which are an existing file name)
bvals: (a list of items which are an existing file name)
bvecs: (a list of items which are an existing file name)
converted_files: (a list of items which are an existing file name)