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
'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)
        flag: -a
args: (a string)
        Additional parameters to the command
        flag: %s
collapse_folders: (a boolean, nipype default value: True)
        flag: -c
config_file: (an existing file name)
        flag: -b %s
convert_all_pars: (a boolean, nipype default value: True)
        flag: -v
date_in_filename: (a boolean, nipype default value: True)
        flag: -d
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
events_in_filename: (a boolean, nipype default value: True)
        flag: -e
gzip_output: (a boolean, nipype default value: False)
        flag: -g
id_in_filename: (a boolean, nipype default value: False)
        flag: -i
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
nii_output: (a boolean, nipype default value: True)
        flag: -n
output_dir: (an existing directory name)
        flag: -o %s
protocol_in_filename: (a boolean, nipype default value: True)
        flag: -p
reorient: (a boolean)
        flag: -r
reorient_and_crop: (a boolean, nipype default value: False)
        flag: -x
source_in_filename: (a boolean, nipype default value: False)
        flag: -f
spm_analyze: (a boolean)
        flag: -s
        mutually_exclusive: nii_output
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

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)