I have an interface in which I would like to decompress a .nii.gz
to .nii
before passing it to an SPM
function. (I know I could create a Gunzip()
node but I would prefer to do this without creating an additional node if possible)
A very simplistic case: let’s say the user inputs a .nii.gz
file and I want the file to be decompressed before it is passed to fslmaths
to be binarized.
class BINInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, argstr="%s -bin")
class BINOutputSpec(TraitedSpec):
out_file = File(exists = True)
class BIN(FSLCommand):
input_spec = BINInputSpec
output_spec = BINOutputSpec
_cmd = 'fslmaths'
I don’t really know how to go from here and define a function that can take the in_file
and convert it to .nii
before running the fslmaths
command. Should I be using _format_arg
for this?