Input Images

Most of the CEST Analysis requires several images to be acquired with different frequency offsets relative to the water resonance frequency. These can be supplied in:

• A single input image containing all frequency offsets and slice locations.
• Multiple input images, with each image containing all slice locations for one frequency offset. The number of input images will equal the number of frequency offsets.
• Multiple input images, with each image containing all frequency offsets for one slice location. The number of input images will equal the number of slice locations.

Select the appropriate button in the input image configuration. You also need to set the number of physical slice locations using the spinner: . This is used as an additional check that the input configuration is correct.

Also select if either:

• You have a single input image with multiple slice locations, and the different frequency offsets are contiguous (i.e., all frequency offsets for the first slice are followed by all frequency offsets for the second slice, etc.)
• You have multiple input images and each of the input images contains all frequency offsets for one slice location.

The standard masking options apply if you want to mask the input image(s):

• Set an intensity threshold: only pixels with intensity above the threshold will be processed.
• Apply an image mask: only pixels in the mask image where the intensity is above zero will be processed.
• Apply an ROI mask: only pixels inside ROIs will be processed.

Inputting the frequency offsets

CEST analysis can be informed about the frequency offsets in one of 3 ways:

• If you want to try to get the frequency offsets automatically from the input images, then select

  Currently, frequency offsets can only be gotten automatically from Bruker DICOM images or images converted from Bruker DICOM images.

• Input as a comma-separated list of offset frequencies (in parts-per-million [ppm]). Deselect , then select . Enter the frequency offsets (in ppm relative to water) as a comma-separated list, e.g.: .

• Input the first and last frequency offsets, and the number of evenly-spaced frequency offsets. Deselect , then select . Specify the frequency offsets (in ppm relative to water) by entering:

  • The first frequency offset (i.e., the frequency offset for the first slice of the input image(s)).
  • The last frequency offset (i.e., the frequency offset for the last slice of the input image(s)).
  • The number of unique frequency offsets.

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You can now select the tab for the type of CEST analysis you want to perform.