itk_convert

convert between medical image formats using ITK (MINC, NIfTI, NRRD, etc.)

itk_convert <input> <output> [options]

DESCRIPTION

itk_convert converts medical image volumes between file formats supported by the Insight Toolkit (ITK). Supported formats include MINC (.mnc), NIfTI (.nii, .nii.gz), NRRD (.nrrd, .nhdr), Analyze (.hdr/.img), MetaImage (.mha, .mhd), and other ITK-recognized formats. The conversion format is determined automatically from the file extensions of the input and output arguments.

The tool can change voxel data types during conversion, normalize intensity values, invert axis directions, apply compression, and handle special modalities such as diffusion-weighted imaging (DWI) and diffusion tensor imaging (DTI).

OPTIONS

--verbose

Print verbose information during processing.

--clobber

Overwrite the output file if it already exists.

--quiet

Suppress all informational output.

--char

Store output voxels as signed 8-bit characters.

--byte

Store output voxels as unsigned 8-bit bytes.

--short

Store output voxels as signed 16-bit short integers.

--ushort

Store output voxels as unsigned 16-bit short integers.

--int

Store output voxels as signed 32-bit integers.

--uint

Store output voxels as unsigned 32-bit integers.

--float

Store output voxels as 32-bit floating point.

--double

Store output voxels as 64-bit double-precision floating point.

--inv-x

Invert the X axis direction cosine.

--inv-y

Invert the Y axis direction cosine.

--inv-z

Invert the Z axis direction cosine.

--center

Set the volume origin to the center of the volume.

--normalize

Normalize voxel intensity values to the range [0, 1].

--comp

Write compressed output (e.g., gzip for NIfTI).

--clamp

Clamp voxel values to the valid range of the output data type.

--dwi

Treat the input as a diffusion-weighted image volume.

--dti

Treat the input as a diffusion tensor image volume.

--use-b-matrix

Use the B-matrix instead of gradient directions for DWI/DTI conversion.

--nii-scale

Apply NIfTI intensity scaling (scl_slope and scl_inter) during conversion.

--spacing x,y,z

Override the output voxel spacing with the given values (comma-separated, in mm).

--labels

Treat the volume as a label (discrete integer) image, using nearest-neighbour semantics where applicable.

--relx

Relax file format checks to allow non-standard header content.

EXAMPLES

Convert a MINC volume to compressed NIfTI format:

itk_convert input.mnc output.nii.gz --comp

Convert a NIfTI file to MINC with unsigned short data type:

itk_convert input.nii output.mnc --ushort --clobber

Convert with axis inversion and normalization:

itk_convert input.mnc output.nii --inv-z --normalize

Convert a diffusion tensor image from NRRD to MINC:

itk_convert input.nrrd output.mnc --dti --float

AUTHOR

Vladimir S. Fonov - Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright (C) Vladimir S. Fonov, McConnell Brain Imaging Centre, McGill University.

SEE ALSO

itk_resample, mincconvert, itk_convert_xfm, mincreshape