itkimage2segimage
tool can be used to save the volumetric segmentation(s) stored as labeled pixels using any of the formats supported by ITK, such as NRRD or NIFTI, as a DICOM Segmentation Object (further referred to as SEG).labelID
defines the value of the segment in the segmentation file that will be assigned attributes listed.labelID
is not stored in the output DICOM! The sole purpose of this attribute is to establish the connection between the labels encoded in the input ITK files and the metadata describing those labels (segments). The output DICOM files will have segments numbered consecutively starting from 1, and labelID
should not be used to encode the type of structure being segmented. What the segment actually represents is indicated by a set of "codes": SegmentedPropertyCategoryCodeSequence
, SegmentedPropertyTypeCodeSequence
, and SegmentedPropertyTypeModifierCodeSequence
(optionally), as discussed below.SegmentLabel
can be anything that fits within a 64 character string.CodeMeaning
of SegmentedPropertyTypeCodeSequence
):SegmentDescription
is a short free-text description of the segment.SegmentAlgorithmType
can be assigned to MANUAL
, SEMIAUTOMATIC
or AUTOMATIC
. If the value of this attribute is not MANUA
, SegmentAlgorithmName
attribute is required to be initialized!RecommendedDisplayCIELabValue
attribute can be used to specify the color in CIELab color space.SegmentedPropertyCategoryCodeSequence
and SegmentedPropertyCategoryCodeSequence
are attributes that should be assigned code tuples to describe the meaning of what is being segmented.CodeValue
, CodingSchemeDesignator
and CodeMeaning
. CodingSchemeDesignator
defines the "authority", or source of the code. Each CodeValue
should be unique for a given CodingSchemeDesignator
. CodeMeaning
is a human-readable meaning of the code. DICOM defines several coding schemes recognized by the standard listed in PS3.16 Section 8.SegmentedPropertyTypeCodeSequence
are predicated on the value of the SegmentedPropertyCategoryCodeSequence
. It is also possible to define SegmentedPropertyTypeModifierCodeSequence
that can be used , for example, to define the laterality. In some situations, it is appropriate or required to also specify anatomical location of the segmentation (e.g., organ a tumor was segmented). The latter can be achieved using AnatomicRegionSequence
and AnatomicRegionModifierSequence
coded attributes.