I have been trying to segment the rodent brain using rbm and fsl. At first, I deduct some planes to make the image more precise (deduction from fsl), then I re scale the dimensions to 0.1 pixels in x, y and z planes. Finally I do the segmentation. But the image becomes blank every time I try to segment it.
# For adding/deducting planes from the image: 3dZeropad -A -41 -R -22 -L -34 2427_copy.nii.gz -prefix 2427_zeropad.nii.gz 3dZeropad -A -41 -R -22 -L-34 -prefix 2427_zero.nii.gz 2427_copy.nii.gz # For re scaling: 3drefit -xdel .1 -ydel .1 -zdel .1 2427_zero.nii.gz # For the segmentation: rbm 2427_zero.nii.gz mask_zero.nii.gz
My concern is it’s giving me a blank image after segmentation. I would appreciate it if someone could let me know what I am supposed to do change. Do I reorient the image or swap the dimensions?