Brain Finder - Calculating the BPF

Note: if you have previously created the brain outline, and saved the ROIs to disk, you can simply reload them from disk at this stage, without re-finding them.

When performing fully-automated analysis, the BPF calculation has two parameters that may need to be adjusted, depending on the type of image being analysed.

Note: fully-automated analysis is strongly recommended to aid consistency of BPF measurements.

1. Fitting Separate Grey- and White-Matter Peaks

   Some, more heavily T₁-weighted, images have two peaks for the parenchyma: one for the grey matter, and one for the white matter. If this is the case for your images, then select

   To check whether this setting is appropriate for your images, you need to view the image intensity histogram of the brain. First mask the image to isolate just the brain and CSF. Then view the intensity histogram for the whole image by opening the image statistics dialog. Below is a 3-D FLASH image that requires separate peaks fitted to the grey and white matter.

   Heavily T1-weighted 3-D FLASH image.	Intensity histogram for the image to the left (all slices), with separate peaks for CSF, grey matter and white matter.

2. Setting the Threshold Between CSF and Parenchyma

   When calculating the BPF, an intensity threshold is set which divides CSF from brain: all pixel with intensity below the threshold are considered to be CSF, and all those with intensity above are considered to be brain. The threshold is located between the histogram peaks for the CSF and brain (or grey-matter, if separately fitting GM and WM). The exact threshold location is determined by the CSF/brain threshold fraction:

   

   Use the slider to set a value between 0 and 1. A value of 0 will put the threshold at the position of the CSF peak in the intensity histogram. A value of 1 will put the threshold at the position of the brain (or GM) peak in the intensity histogram. A setting of 0.5 (the default value) will put threshold half way between the CSF and brain peaks.

   If you find that too much brain tissue is being classed as CSF (the BPF is too low), then reduce the threshold fraction. Conversely, if you find that too much CSF is being classed as brain tissue (the BPF is too high), then increase the threshold fraction.

Note: whatever setting you use your images, for both cross-sectional and serial studies it is important to maintain the same setting for all patients scanned on any given scanner. Because of differences in contrast from scanner to scanner, it may be necessary to adjust the settings on a scanner-by-scanner basis, but for serial studies it is imperative that the same setting is always used for any given patient/scanner. You also have three further options:

• If you do not want the CSF / parenchyma intensity threshold to be selected automatically, and you have another method for determining the threshold, then select:

  

  and enter the threshold in the field provided. Any pixels with intensities above the threshold will be counted as parenchyma, and those below will be counted as CSF.
  Note: when the threshold is set manually, no further image uniformity correction is performed as part of the BPF computation.
• If it is clear from the result that BPF calculation is problematic, then you can help Jim to find the BPF by manually setting the initial guesses for the CSF, and parenchyma peak positions. Click the "Set initial guesses for peak locations manually" check box.

  

  Using the whole-brain intensity histogram as a guide, enter your estimates of the peak positions for the CSF and parenchyma or (if you are fitting grey and white matter peaks separately) grey and white matter peaks.
• For the purposes of verification, you can create images showing the distribution of parenchyma and CSF. To create these images, select . Images are created with the original image name plus suffixes "CSF" and "Brain" (or, if you are fitting grey and white matter peaks separately) "GM" and "WM".

Finally, click on the button. This fits a distribution of intensities to the histogram, assigns the peaks to CSF and parenchyma (or CSF, grey matter and white matter, if selected) and then chooses the intensity threshold between the CSF and parenchyma (or grey matter) peak positions according to the BPF CSF/brain threshold fraction (see above). The threshold is then applied to separate CSF from parenchyma, and the BPF calculated as:

• If you choose to write to a text file report, then a File chooser will appear, for you to choose a log file name. The default file extension for log files is ".log". If the chosen file already exists, a BPF report entry will be appended to the log file. The format of a Brain Finder log file is given in the file formats section.
• If you choose to write to a PDF file report, then a File chooser will appear, for you to choose a PDF file name. If the chosen file already exists, a Brain Finder report entry will be appended to the PDF file.
• Select the "Dismiss" option if you do not want to write a report.

A graph will also pop up showing the quality of the fit that is used to estimate the CSF/brain threshold.