CLI

Installing MedVol adds the medvol command.

medvol convert

Convert a file or DICOM directory and print the report.

medvol convert ct.nii.gz ct.mla
medvol convert dicom_dir/ ct.nii.gz --dicom-stacks largest --world-frame ras
medvol convert ct.mla ct.mha --on-loss error          # fail instead of dropping what MetaImage cannot store
medvol convert ct.mla out_dir/ --target-format dicom  # re-emit the original DICOM series

option	meaning
--source-format NAME	input format, if it cannot be detected
--target-format NAME	output format, if the extension does not say (e.g. dicom)
--nifti-form, --nifti-form-disagreement, --nifti-form-tolerance-mm, --nifti-no-codes	NIfTI policies
--reorient, --world-frame	orientation
--dicom-tilt, --dicom-irregular-spacing, --dicom-stacks, --dicom-rescale	DICOM policies
--vector-frame	vector frame
--on-loss, --layout	writing

Writing a DICOM SEG needs the referenced series and is done from Python (Usage).

medvol inspect

Print a summary of a file or DICOM directory in the MLArray vocabulary: shape, dtype, values, axes, spaces and warnings. It takes --format and the same policy options.

medvol inspect ct.nii.gz

ct.nii.gz: nifti, 1 image(s)
[0] shape (7, 6, 5) int32, values measurement
    axes: z:space, y:space, x:space
    space patient: spacing (0.5, 1.0, 2.0), origin (12.5, -30.25, 47.0), letters RIP

medvol formats

List the installed format plugins and their extensions.

mlarray_convert

MLArray's mlarray_convert INPUT OUTPUT uses MedVol with the same policy options. mlarray_header prints the metadata of a .mla file (MLArray CLI).