Fixing Voxel Dimensions

Different scanner vendors (Philips, Siemens, GE, Toshiba, etc) and different type types (NIFTI, DICOM, etc) can sometimes corrupt the dimensions of the voxels.

You will need the following information to fix bit values:

  • Voxel Dimensions: these are in-plane (x/y) dimensions for the voxels in units of mm.

Obtaining Distance Rescaling

You need to determine (1) the scale of the phase image and (2) the correct scale of the phase image. There are several ways to do this.

  • Check DICOM header. This will vary depending on your scanner vendor and DICOM viewer. Assuming a Philips phase image and using HOROS:

    1. Open HOROS and find image you want to manipulate. Select and highlight the image.

    2. Open MetaData of the Image that has been selected (File→ MetaData)

    3. Open dropdown menu 'Per-frameFunctionalGroupSequence' (String- 52009230).

    4. Open third dropdown menu arrow titled 'Item'.

    5. Open the section titled 'PixelMeasuresSequence'

    6. Open 'Item'

    7. Open 'Pixel Spacing'. These values are the dimension of the voxels, typically between 0.25-1.00 mm.

  • Assume voxel dimensions. If you know the voxel dimensions, you can skip this step and use the values.

Applying Distance Rescaling

  1. Open ImageJ

  2. Open the image you want to manipulate

  3. Select Analyze→Set Scale. Change 'Distance in Pixels' equal to 1 and enter the known distance (from Obtaining Distance Rescaling)

  4. Enter the Distance in Pixels and Known Distance, select OK.

  5. To save your fixed image as a tiff format file. Select: File→Save as→Tiff