I have created some FA maps using the MRTrix suite, but after closer inspection of the images there are multiple ‘holes’ in the map, where the value is NaN / ?. I have attached some screenshots of the ‘holes’ in question. What could these ‘holes’ be? They only appear in the FA map, the original image & mask image do not have anything that could resemble these holes.
The commands I used to create the map are as follows:
dwi2tensor input_file output_name_fa -mask mask_file_name
tensor2metric input_file (output of the dwi2tensor command) -fa output_fa_map -adc output_md -mask mask_file_name
