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)
        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 newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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
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)
        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
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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)

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_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.compress = 'i'
>>> converter.inputs.single_file = True
>>> converter.inputs.output_dir = '.'
>>> converter.cmdline 
'dcm2niix -b y -z i -x n -t n -m n -f %t%p -o . -s y -v n functional_1.dcm'
>>> flags = '-'.join([val.strip() + ' ' for val in sorted(' '.join(converter.cmdline.split()[1:-1]).split('-'))])
>>> flags 
' -b y -f %t%p -m n -o . -s y -t n -v n -x n -z i '

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]
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
compress: (u'y' or u'i' or u'n', nipype default value: i)
        Gzip compress images - [y=pigz, i=internal, n=no]
        flag: -z %s
crop: (a boolean, nipype default value: False)
        Crop 3D T1 acquisitions
        flag: -x
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
has_private: (a boolean, nipype default value: False)
        Flag if text notes includes private patient details
        flag: -t
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
merge_imgs: (a boolean, nipype default value: False)
        merge 2D slices from same series
        flag: -m
out_filename: (a unicode string, nipype default value: %t%p)
        Output filename
        flag: -f %s
output_dir: (an existing directory name)
        Output directory
        flag: -o %s
single_file: (a boolean, nipype default value: False)
        Convert only one image (filename as last input
        flag: -s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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
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)