Slice exclusion

I have some neonatal cervical spinal cord data and I would like to exclude slices belonging to the brain , excluding everything that is not spinal cord. Do you suggest a specific tool in order to do this?
Thank you,

Hi Rosella,

There’s quite a number of different ways of approaching a task like this:

  • mrconvert -coord option can be used to specify which voxel locations to retain along a given axis; so specify the axis corresponding to slices (likely 2), and provide a number range that corresponds to your desired FoV.

  • mrcrop: Either the -axis option, specifying the indices of the first and last slices to retain, or by generating a mask image of your structure of interest and running this command on your DWI data whilst providing such a mask via the -mask option.

  • The FSL command standard_space_roi is intended for this sort of operation; but you would require an appropriate template image and corresponding mask to be able to make use of it.