DICOM

Class: NodeExportDICOM

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Convert and save connected images to DICOM files on disk. DICOM is a standardized image format for storing and sending medical images from many different modalities. With each image comes extensive metadata information regaring e.g. imaging modality, imaging settings, scan time and date, patient information etc. Many metadata tags are specific to one modality, which makes a function that fully adheres to the DICOM standard difficult to implement. This is important if images are imported in other software such as dose planning programs or sent to a DICOM node or PACS for storage.

For this reason, MICE Toolkit supports three DICOM image export modalities; CT, MRI, and RTDOSE.

Quantization errors in DICOM

DICOM can only save pixel data in integer values between 0 and 65,535. To represent decimal values, a linear transformation is applied to the pixel data. The slope and intercept of this transformation is calculated so that the range of integer values in the dicom image covers the dynamic range of the values being stored. For large pixel ranges this method will lead to quantization error. To minimize the ammount of quantization, make sure you limit the range of values in the images. Voxels with extreme values outside the window of interest will lead to a large quantization error. This is illustrated in the figure below.

quantization error

The figure shows two image histograms after a linear transformation. The images are identical, except for a few outlier voxel values of 100 in the right image. In this toy example, there are 50 gray levels available. If the span of intensities is [0 - 15], the quantization error is quite small. However, if the span is [0 - 100], the quantization error is much larger.

Example Workflows

Export to DICOM examples

Inputs

In

One or more images.

Type: Image4DFloat, Required, Multiple

Settings

Export

Modality Selection

Defines what the resulting DICOM images modality should be.

Values: MR, CT, RTDOSE

Series Description Text

Defines what the resulting DICOM images series description should be.

Slicewise Slope/Intercept Boolean

If TRUE, the intercept and slope will be recalculated for each slice, this might lead to a smaller quantization error.

Force Integer Values Boolean

If TRUE, the node will try to save voxel values as integer values (if modality is set to RTDOSE this setting will be ignored). The slope will always be 1, intercept will be adjusted. Voxel values will be rounded to the nearest integer value. If the total span of values in the image is more than 65535, values outside that span will be truncated.

WARNING: Using this feature might drastically change your data and should only be used if you fully understand what it does.

Protocol Name Text

Name of the protocol if applicable.

Set Image Name Boolean

If TRUE, the specified image name will be used to name the image(s). If more than one image is connected, a counter will be added to the end of the name.

Image Name Text

The new image name, will be used to name the image if the “Set Image Name” option is selected.

Path Text

Set the output directory of the node.

Note: This parameter will be overridden if you use this node for batch calculations.

Metadata

Override Metadata Boolean

If TRUE, the metadata for the exported files will be set to the fields in this category. The patient metadata from the input images will not be used if this is set.

Patient ID Text

Set the new patient ID.

Patient Name Text

Set the new patient name.

Frame of Reference Text

Set the new frame of reference.

Study Date Date

Set the new study date.

DICOM Remote

Send to remote storage Boolean

If TRUE, the files will be sent to a remote DICOM storage instead of being saved to disk.

Host Text

The IP or hostname of the remote DICOM storage.

AE Title Text

The AE title of the remote DICOM storage.

Port Integer

Port to use when connecting to the remote dicom storage.

See also

DICOM Standard Browser for a complete list of all DICOM tags.

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