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 14, 2020 12:41PM
Hi,

Yes, the TEST worked. Here are the three steps:

A) afni –ver output:
(base) Mac-Pro-de-Neurociencia:SUMA neurociencia$ afni -ver
Precompiled binary macos_10.12_local: Oct 2 2020 (Version AFNI_20.3.00 'Vespasian')

B) Surf Smooth response:
(base) Mac-Pro-de-Neurociencia:SUMA neurociencia$ SurfSmooth -spec std.141.FT_lh.spec -surf_A std.141.lh.smoothwm.gii -met HEAT_07 -input std.141.lh.sulc.niml.dset -target_fwhm 6 -Niter -1 -output TEST.niml.dset
++ Notice SUMA_SigForFWHM (SUMA_GeomComp.c:7400 @11:01:03):
Low Sigma/AvgLe, increased it to 0.500
Expected niter now: 89
Kernel Bandwidth / Average Edge Distance = 0.500000/0.816885 = 0.408443
Corresponding Kernel Numerator = 0.135335
++ Notice SurfSmooth (SUMA_SurfSmooth.c:2220 @11:01:03):
Smoothing kernel bandwidth (sigma) = 0.408443

#Final smoothing parameters from input:
#Niter Sigma OutputFWHM
0 0.4084 6.000

++ Notice SUMA_WriteSmoothingRecord (SUMA_GeomComp.c:7023 @11:01:03):
Writing FWHM progression history to TEST.niml.dset.1D.smrec ...


C) Commands used and response:
(base) Mac-Pro-de-Neurociencia:SUMA neurociencia$ 3dVol2Surf -spec std.141.Alejandro_rh.spec -surf_A std.141.rh.smoothwm.gii -surf_B std.141.rh.pial.gii -map_func ave -f_steps 15 -f_index voxels -sv Alejandro_SurfVol_Alnd_Exp+orig -grid_parent Alejandro_decon_Nopal.TENT.int.psc+orig -oob_value 0.0 -oob_index 0.0 -out_niml rh_Alejandro_decon_Nopal.TEMT.ave_.niml.dset
** surface name 'std.141.rh.smoothwm.gii' not found


This is previous step tan SurfSmooth. The thing is, the file std141.rh.smoothwm.gii is there in SUMA, but I can only advance from this step to SurfSmooth if I use my created mesh140.rh.smoothwm.asc. And then, in that step, SurfSmooth falls.

Thank you very much.
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