MATLAB Answers


Incorrect voxel values after export from Osirix

Asked by Tristan
on 21 Jan 2013


When I export CT scan DICOMS from Osirix and import into MATLAB the intensity values are being skewed. This was confirmed by uploading a slice of original CT data from the scanner (calibrated to HU), and then uploading the same slice after first importing the scan into Osirix and exporting it back out. Once in MATLAB, the Osirix array had to be corrected for slope and intercept according to the values specified in the metadata. I then subtracted the Osirix array from the original to confirm that the intensity values were the same. The result contained residual signal, particularly in areas of higher attenuation (ie bone), indicating that the slice which had been exported from Osirix did not contain the same intensity values as the original. This difference can also be seen visually when comparing the two arrays using imshow.

Most available information I have found on similar issues indicates that correcting for slope and intercept after export from Osirix or certain other DICOM viewing software should yield true HU. This is an important issue because I will be performing quantitative analysis on these slices and need to be confident that the intensity values we are working with reflect the true results of our CT scan.

Any help or advice in approaching this problem, either from the MATLAB or Osirix side, would be greatly appreciated. Thanks.


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