I am trying to downsample a brain mask derived from a structural T1 volume. I want the brain mask to match my functional data dimensions (48 64 48) so that when performing FSL melodic ICA only voxels from the brain are taken into account. Is this possible with FSL?
Hi @Ibai_Azpeitia_Loiti1, that would be possible after you have registered your functional data to the structural. You can invert the functional->structural transformation, and then transform a structural mask into functional space.
However, another option is to perform brain extraction independently on the functional data. In fact, this is the default behaviour if you are using the MELODIC GUI.
In my case I am performing FSL’s melodic from the command line as the GUI has been giving me errors (the data was preprocessed outside FSL).