interfaces.dcm2nii¶
Dcm2nii¶
Wraps command dcm2nii
Uses MRIcron’s dcm2nii to convert dicom files
Examples¶
>>> tmp = getfixture('tmpdir')
>>> old = tmp.chdir() # changing to a temporary directory
>>> from nipype.interfaces.dcm2nii import Dcm2nii
>>> converter = Dcm2nii()
>>> converter.inputs.source_names = [os.path.join(datadir, 'functional_1.dcm'), os.path.join(datadir, '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'
>>> os.chdir(old.strpath)
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
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: ('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)
Dcm2niix¶
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()
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]
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
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)
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
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
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)