SurfSmooth -surf_B option

AFNI Message Board
1

Hello,

Is there an advantage in SurfSmooth to passing multiple surfaces using the -surf_A, surf_B commands. In the afni_proc generated example, -surf_A is used to specify the smoothwm surface. I have seen some examples where both smoothwm and pial are passed with surf_A and surf_B, respectively. How does the program behave differently if two surfaces are given instead of one. I’ve pasted two sample calls below:


SurfSmooth -spec /workingdir/Nifti/derivatives/sourcedata/freesurfer/fsaverage/SUMA/fsaverage_lh.spec \
        -surf_A smoothwm \
        -input $subj.r$run.hemi-${hem}.tcat.func.gii \
        -met HEAT_07 \
        -target_fwhm 9.0 \
        -blurmaster rm.errts.$subj.r$run.hemi-${hem}.func_REML.gii \
        -output $subj.r${run}.hemi-${hem}.blur.func.gii



SurfSmooth -spec /workingdir/Nifti/derivatives/sourcedata/freesurfer/fsaverage/SUMA/fsaverage_lh.spec \
        -surf_A smoothwm \
        -surf_B pial \
        -input $subj.r$run.hemi-${hem}.tcat.func.gii \
        -met HEAT_07 \
        -target_fwhm 9.0 \
        -blurmaster rm.errts.$subj.r$run.hemi-${hem}.func_REML.gii \
        -output $subj.r${run}.hemi-${hem}.blur.func.gii

Thanks in advance!

2

Hello,

I would not expect -surf_B to even be looked at by SurfSmooth. Can you point out where you have seen such an example?

There should only be one surface to alter and estimate the smoothness over, so it seems that -surf_B should not be used.

  • rick
3

Thanks so much, Rick. I saw this used in some older posts on the message board. Here’s the link for one: https://afni.nimh.nih.gov/afni/community/board/read.php?1,78618,78618#msg-78618

It sounds like those previous users didn’t need to provide -surf_B. Is that correct? Thanks again!

-Anthony

4

That is right, -surf_B should not be needed. And if you notice Ziad’s “simpler command” in his last comment, there was no -surf_B option included.

  • rick
5

Thanks, Rick!