I am trying to run 3DLocalstat on AFNI I wrote 3dLocalstat (filename) -nbhd ‘SPHERE(3)’ -stat mean -automask -prefix (outputname) but the error message below appeared,
FATAL ERROR No -stat options given?
But I have inserted the -stat commands in the line. Is there any way to solve this problem?
Thank you very much.
I think the code syntax is incorrect. The input filename has to be at the end of the list of command line options and arguments, like:
3dLocalstat -nbhd 'SPHERE(3)' -stat mean -automask -prefix DSET_OUTPUT DSET_INPUT
How does that work for you?
Thnaks it worked! It result in a +orig.BRIK file, how do I open and see this file? Thanks again
AFNI I/Os BRIK/HEAD format, as well as NIFTIs. If you would like the output to be a NIFTI file, then just include that extension in the output file prefix, such as:
3dLocalstat -nbhd 'SPHERE(3)' -stat mean -automask -prefix DSET_OUTPUT.nii.gz DSET_INPUT
Just to note, there are some useful getting-to-know-AFNI and general MRI/FMRI analysis teaching materials here:
… and here: