tSNR calculation

Hi there,

I’m looking to calculate tSNR values and have used the following syntax, as per this post:

3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]"
3dTstat -stdev -prefix rm.noise.all errts.${subj}_REML+tlrc"[$ktrs]"
3dcalc -a rm.signal.all+tlrc
-b rm.noise.all+tlrc
-c full_mask.$subj+tlrc
-expr ‘c*a/b’ -prefix TSNR.$subj

Now that I have TSNR.$subj files, I can visually inspect them for signal loss, but how can I extract the tSNR values of interest from these newly generated files?


You can compute the average TSNR with this command:

3dmaskave -quiet -mask full_mask.$subj+tlrc TSNR.$subj+tlrc

Consider the QC reports generated by gen_ss_review_scripts.py that will include this information and lots more. These reports can be automatically generated with the afni_proc.py option “-html_review_style pythonic”

Exactly what I was looking for - thanks, Daniel!