surf.smooth.params.1D giving extra zeros with 1dcat

AFNI Message Board
1

Hi, I’ve been getting errors with afni_proc, where it fails on the blur step. After a bit of digging, the problem seems to be that the file that’s created to estimate the blur parameters (surf.smooth.params.1D) is giving some leading zeros when read by 1dcat, which means that the afni_proc script is asking for a sigma of zero.

The final lines of the afni_proc output are:


if ( ! -f surf.smooth.params.1D ) then
set params = `1dcat surf.smooth.params.1D`
1dcat surf.smooth.params.1D
SurfSmooth -spec /afm01/P007/SUMA/std.141.P007_lh.spec -surf_A smoothwm -input pb03.P007.surf.lh.r02.surf.niml.dset -met HEAT_07 -Niter 0 -sigma 0 -output pb04.P007.surf.lh.r02.blur.niml.dset
Error SUMA_SurfSmooth_ParseInput:
Unexpected combo: fwhm -1.000000, tfwhm -1.000000 , sigma 0.000000

And when I look at the surf.smooth.params.1D file I get:


1dcat surf.smooth.params.1D 
0 0 0 0 0 0 0
19 0.357 -1 0 0 0 0

I’m using the same afni_proc code that worked without this issue at my previous institution (a few years ago now). I’m trying this on a new setup (using https://www.neurodesk.org/docs/neurodesktop/), so I’m not sure if it’s something to do with my setup, or a change in the afni code behaviour. Any thoughts on what the problem might be? Thanks.

2

There might be a problem before then. What is the output if you skip ‘1d’?

cat surf.smooth.params.1D

  • rick
3

The output is:


cat surf.smooth.params.1D 
Comment: #!ascii version in FreeSurfer format (SUMA)
#Final smoothing parameters via master:
#Niter     Sigma    OutputFWHM
    19       0.3570     -1.000
4

Hmmm, that “Comment:” text should not be there.

Do you have the text output from running the proc script, something like output.proc.SUBJECT?

If possible, would you be able to send that to me via email, along with the actual proc.* script?

Thanks,

  • rick