3dLocalstat Error No-stat options given?

AFNI Message Board
1

Good afternoon,

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.

Jacob

2

Hi, Jacob-

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?

–pt

3

Hi pt,

Thnaks it worked! It result in a +orig.BRIK file, how do I open and see this file? Thanks again

4

Hi-

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:
https://www.youtube.com/c/afnibootcamp
… and here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/educational/main_toc.html

–pt