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ImageJ macro to calculate CT helical slice thickness - new version
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Category Diagnostic Imaging
Submitted by dplatten
Author's Name
David Platten
Distributed with custom license file? No
Published
Mon May 20, 2013 12:03 pm

An ImageJ macro to calculate the helical slice thickness from a CT scan along a rod containing a thin gold disc. The method is based on that used by ImPACT. Note: this macro may not work correctly on a bead embedded in a large phantom.

Expects a directory of DICOM images from a helical scan run through a thin metal disc or a very small metal bead. The reconstruction interval should be around 1/10 of the slice thickness. For example, if the reconstructed slice thickness is 3 mm then you need to set the reconstruction interval to 0.3 mm.

The phantom can be a thin gold disc embedded in a Perspex rod, similar to the one that ImPACT uses. Alternatively the method may work by scanning through a small metal bead, provided that the bead is much smaller than the reconstructed slice thickness. However, the routine may fail with this type of test object as it tries to locate the centre of the test object using a centre-of-mass calculation; this may result in the incorrect positioning of the ROI if the test object occupies the whole image.

For each image in the series the centre of mass of pixels that have a value of >= max / 2 is calculated. A circular ROI is then centred at this position and the mean pixel value calculated. The z-position of the image is recorded. Once all images have been examined, the background is subtracted from every point (actually the minimum mean ROI value), and then the values are normaised to the maximum value. The full-width at half-maximum of the profile is then calculated.

There can be ".txt", ".csv" or "dcminf" files in the directory with your images, but nothing else. Any other file in the directory will cause the routine to fail.


Member reviews

Review #16: Average by darrendemers12 on Thu Aug 13, 2015 8:00 am


ImageJ macro to calculate CT helical slice thickne

The phantom can be a thin gold disc embedded in a Perspex rod, similar to the one that ImPACT uses. Alternatively the method may work by scanning through a small metal bead, provided that the bead is much smaller than the reconstructed slice thickness. However, the routine may fail with this type of test object as it tries to locate the centre of the test object using a centre-of-mass calculation; this may result in the incorrect positioning of the ROI if the test object occupies the whole image.
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