Image Fitting - Speeding Up Fitting

In certain situations, for example to avoid fitting to background noise, it may be useful to exclude some pixels from the fitting procedure. There are four ways to exclude (mask out) pixels:

Different ways to mask out fitting to certain
                                                   pixels

These are:
  1. Mask using an intensity threshold to exclude pixels based on their intensity, enter an intensity threshold. If all the pixels at one position in the input images are above the threshold, fitting is performed for that pixel as normal.

  2. Mask using Brain Finder use the Brain Finder exclude pixels outside the brain. If you are analysing human brain images, it may be possible to use the Brain Finder tool to first isolate the brain, and then fit to pixels only inside the brain. The Brain Finder will be applied to the first image in your series with different independent variable values, so the success of this depends on whether it has a contrast suitable for use with Brain Finder. To use this, enter a "Threshold fraction" that has previously been found to be suitable for your image (by experimenting with the Brain Finder).

  3. Mask using an image mask to use another image to exclude pixels from fitting. An image mask in an image with the same number of columns, rows and slices of pixels as the images being analysed. For pixels to be fitted, the image mask's pixel intensity is non-zero, and for pixels that are to be excluded from fitting, the image mask's pixel intensity is zero.

  4. Mask using a set of ROIs to use a set of regions-of-interest (ROIs) exclude pixels from fitting. The ROIs are defined on one of the input images. Pixels outside the ROIs are not fitted.

When fitting is not performed in a particular pixel because that pixel is excluded by the masking operation, the intensity in all the output images set to zero for that pixel. This can speed up the fitting considerably. It also make the output images look prettier by excluding the random values output when fitting to noise.

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