Module that provides tools to convert DICOM files.

pydcmio.dcmconverter.converter.add_meta_to_nii(nii_file, dicom_dir, dcm_tags, outdir, prefix='f', additional_information=None)

Add dicom tags to Nifti1 image header.

All selected dicom tag values are set in the ‘descrip’ Nifti header field.

Parameters:

nii_file: str

The nifti image to fill.

dicom_dir: str

The directory containing the dicoms used to generate the nifti image. We assume here that this folder contains only Dicom files.

dcm_tags: list

A list of 3-uplet of the form (name, tag, stack_values) that will be inserted in the ‘descrip’ Nifti header field. If we want to stack all the Dicom dataset values, the ‘stack_values’ option mist be set to True.

outdir: str

The destination folder.

prefix: str (optional, default ‘f’)

The output image name prefix.

additional_information: dict (optional, default None)

A free dictionary items to be inserted in the ‘descrip’ image header field.

Returns:

filled_nii_file: str

The nifti image with filled header.

pydcmio.dcmconverter.converter.dcm2nii(input, o, b)

Dicom to nifti conversion using ‘dcm2nii’.

You can specify all the ‘dcm2nii’ command options as input function parameters.

The basic usage is: dcm2nii <options> <sourcenames>

Options: a Anonymize [remove identifying information]: Y,N = Y b load settings from specified inifile, e.g. ‘-b C:set 1.ini’ d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = N e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = N f Source filename [e.g. filename.par -> filename.nii]: Y,N = N g gzip output, filename.nii.gz [ignored if ‘-n n’]: Y,N = Y i ID in filename [filename.dcm -> johndoe.nii]: Y,N = N n output .nii file [if no, create .hdr/.img pair]: Y,N = Y o Output Directory, e.g. ‘C:TEMP’ (if unspecified, source directory is used) p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y r Reorient image to nearest orthogonal: Y,N s SPM2/Analyze not SPM5/NIfTI [ignored if ‘-n y’]: Y,N = N t Text report (patient and scan details): Y,N = N v Convert every image in the directory: Y,N = Y x Reorient and crop 3D NIfTI images: Y,N = N

Returns:

files: list of str

the converted files in nifti format.

reoriented_files: list of str

the reoriented converted files in nifti format.

reoriented_and_cropped_files list of str

the reoriented and cropped converted files in nifti format.

bvecs: list of str

the diffusion directions.

bvals: list of str

the diffusion acquisiton b-values.

pydcmio.dcmconverter.converter.dcm2niix(input, o, f='%p', z='y', b='y')

Dicom to nifti conversion using ‘dcm2nii’.

You can specify all the ‘dcm2niix’ command options as input function parameters.

The basic usage is: dcm2niix [options] <in_folder>

Options: b: BIDS sidecar (y/n, default n) f: filename (%a=antenna (coil) number, %c=comments, %d=description, %e echo number, %f=folder name, %i ID of patient, %m=manufacturer, %n=name of patient, %p=protocol, %s=series number, %t=time, %u=acquisition number, %z sequence name; default ‘%f_%p_%t_%s’) h: show help m: merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n) o: output directory (omit to save to input folder) s: single file mode, do not convert other images in folder (y/n, default n) t: text notes includes private patient details (y/n, default n) v: verbose (y/n, default n) x: crop (y/n, default n) z: gz compress images (y/i/n, default n) [y=pigz, i=internal, n=no]

Returns:

files: list of str

the converted files in nifti format.

bvecs: list of str

the diffusion directions.

bvals: list of str

the diffusion acquisiton b-values.

bids: str

BIDS sidecar.

pydcmio.dcmconverter.converter.generate_config(niidir, anonymized=True, gzip=True, add_date=True, add_acquisition_number=True, add_protocol_name=True, add_patient_name=True, add_source_filename=True, begin_clip=0, end_clip=0)

Generate a dcm2nii configuration file that disable the interactive mode.

Parameters:

niidir: str

The nifti destination folder.

anonymized: bool (optional, default True)

If ‘True’ then patient name will not be copied to NIfTI header.

gzip: bool (optional, default True)

If ‘True’ then dcm2nii will create compressed .nii.gz files.

add_date: str (optional, default True)

If ‘True’ then dcm2nii will add the requested element in the output filename.

add_acquisition_number: str (optional, default True)

If ‘True’ then dcm2nii will add the requested element in the output filename.

add_protocol_name: str (optional, default True)

If ‘True’ then dcm2nii will add the requested element in the output filename.

add_patient_name: str (optional, default True)

If ‘True’ then dcm2nii will add the requested element in the output filename.

add_source_filename: str (optional, default True)

If ‘True’ then dcm2nii will add the requested element in the output filename.

begin_clip: int (optional, default 0)

Specifies number of volumes to be removed from the beginning of a 4D acquisition.

end_clip: int (optional, default 0)

Specifies number of volumes to be removed from the end of a 4D acquisition.

Returns:

config_file: str

A dcm2nii configuration file written in the input ‘niidir’ folder.