Creating customized template

It is recommended to use your own customized templates because:

  1. The contrast of your MR images might differ from the existing template.
  2. The demographics of your subject population might differ from those used to generate the existing template.
  3. Each scanner introduces specific non-uniformities in image intensity and inhomogeneities in B0 field.

This function will create a customized template (T1.img) and prior images of gray and white matter and CSF (gray.img/white.img/csf.img). These images are already smoothed with FWHM of 8 mm for use with the subsequent segmentation procedures.

After starting you will be asked to either segment images and create template and prior images or to use previously segmented images to create template and priors. The first option will calculate your template and the priors, but will also save the temporary (warped and the segmented) images. If you have created your template and your are not satisfied with this result you can use the second option to exclude some images from template calculation.

This function will save the following files:

    T1.img customized T1 template, smoothed with FWHM of 8mm
    gray.img gray matter prior image, smoothed with FWHM of 8mm
    white.img white matter prior image, smoothed with FWHM of 8mm
    csf.img CSF prior image, smoothed with FWHM of 8mm

and the temporary files (which can be removed after finishing the template calculation):

    w*.img warped raw image
    w*_seg1.img gray matter of warped image
    w*_seg2.img white matter of warped image
    w*_seg3.img CSF of warped image

Schematic overview about the 2-step segmentation approach. In the first step the customized template is created by averaging all segmented images of the whole sample. In the second step all images are again segmented by using the created template.