interfaces.dcm2nii

Dcm2nii

Link to code

Wraps the executable 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_names: (a list of items which are an existing file name)
        argument: ``%s``, position: -1
        mutually_exclusive: source_dir
source_dir: (an existing directory name)
        argument: ``%s``, position: -1
        mutually_exclusive: source_names

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

Outputs:

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

Dcm2niix

Link to code

Wraps the executable 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() 

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() 

Inputs:

[Mandatory]
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
        argument: ``%s``, position: -1
        mutually_exclusive: source_dir
source_dir: (an existing directory name)
        A directory containing dicom files to be converted
        argument: ``%s``, position: -1
        mutually_exclusive: source_names

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

Outputs:

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