DICOM Rescale (DICOM_RescaleTP)
Author: J. Anthony Parker, MD PhD (J.A.Parker@IEEE.org
Dates: 2007/12/10: First version
Source: The source file, DICOM_RescaleTP.java.
Installation: Download DICOM_RescaleTP.class to the plugins folder and restart ImageJ.  DICOM_RescaleTP is also included in NucMed.zip see NucMed.
Description: This ImageJ PlugIn works on stacks derived from DICOM data which retain the DICOM fields in the slice labels.  (To see if the DICOM fields are present do "Image/Show Info ..." and look for lines that have the following format: "0028,1053  Rescale Slope: 0.589978".)

This plugin is intended primarily for images which have different DICOM rescaling parameters for each slice.  This tends to be true in particular for Nuclear Medicine images, especially PET images.  ImageJ does not use these parameters when reading the data with "File/Import/Image Sequence ...".  Consequently, images in a stack end up being displayed on different scales.  The plugin will also set the display lower threshold to zero.  This can be helpful when processing images, especially CT images where the interesting information is often located at a value around 1000.

The plugin first converts the images using the current calibration.  It then can 1) apply the DICOM "Rescale Intercept" and "Rescale Slope", 2) subtract the lower threshold equal to "Window Center" - 1/2 "Window Width", and 3) set negative values to zero.  It changes pixel values, and produces a new uncalibrated stack.

This plugin alters the raw data, but it puts in a format which can often be useful for further processing.  An alternate would have been to adjust the calibration factors using the DICOM parameters without affecting the pixel values.

Using separate rescaling parameters for each image is useful when trying to fit the data into a byte matrix.  Using this format has not made sense for at least the last decade.  Hopefully, this format will disappear; however, unfortunately it has not been disappearing rapidly.
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