AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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October 07, 2020 09:21PM
Hi, Some months ago I asked for your help on this error

(base) Mac-Pro-de-Neurociencia:Semantic_Priming neurociencia$ tcsh Script3A
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm
-- Error SurfSmooth (SUMA_SurfSmooth.c:2128):
Failed to get mean fwhm


I receive some guidance but the problem was never resolved. So I´m asking your help again.

This is the code I´m trying to run:

foreach conds ("Nopal" "Norel" "Rel" "Xnopal" "Xnorel" "Xrel") ## For each of the conditions in a priming task

foreach h (lh rh) ## For each hemisphere

SurfSmooth -spec $SUMA_path/mesh140.${subj}_"$h".spec \
-surf_A mesh140."$h".smoothwm.asc \
-met HEAT_07 -input $data_path/"$h"_${subj}_decon_$condition.BLOCK.ave_.niml.dset \
-target_fwhm 6 -Niter -1 \
-output $data_path/"$h"_${subj}_decon_$conds.BLOCK.ave_.blur6.niml.dset

end

end



Using a mesh in SUMA with this code:

## Create meshes

foreach h (lh rh) ## For each hemisphere

MapIcosahedron -spec ${subj}_"$h".spec -ld 140 -prefix mesh140. -NN_dset_map $h.aparc.a2009s.annot.1D.roi -all_surfs_spec -verb

end

Please help, I can´t smooth the activations and proceed to the ANOVA analysis.
Subject Author Posted

Still with SurfSmooth error

franciscoara October 07, 2020 09:21PM

Re: Still with SurfSmooth error

ptaylor October 08, 2020 10:56AM

Re: Still with SurfSmooth error

Daniel Glen October 08, 2020 11:59AM

Re: Still with SurfSmooth error

franciscoara October 09, 2020 08:19PM

Re: Still with SurfSmooth error

ptaylor October 09, 2020 09:13PM

Re: Still with SurfSmooth error

franciscoara October 14, 2020 12:41PM

Re: Still with SurfSmooth error

ptaylor October 14, 2020 05:01PM

Re: Still with SurfSmooth error

Daniel Glen October 14, 2020 08:56PM