Thursday, 18 November 2010

Template and other things

I have decided which standard brain that will be included with the tool. It will be the ICBM 2009a non-linear asymmetric template (Copyright (C) 1993-2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University), subsampled to 2x2x2 resolution. This standard brain is included in FSL (avg152T1_brain.nii.gz).

Some limitations for the first version:
  1. The dimensions of the standard template are 91x109x109, subsampled to 2x2x2 mm^3. The coordinate system is Right-to-Left. Images you add have to be in the same space with the same dimensions as the template. This is the standard resolution that comes with SPM and FSL, so it shouldn't be any problems.
  2. All images you add have to be in float format. You need to convert them to float if you have byte format or 16-bit format.
  3. The app will check for this in the image header and only list images that fulfil this requirement. Only uncompressed .nii files will be supported.
One change is that the tool will support thresholding of images. Instead of visualising all voxels above 0 in the same colour, the app will show the images in a jet-map and you will set the threshold yourself. I'm currently adding this feature and I think it will be quite useful.

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