History of AFNI updates  

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May 06, 2022 07:23AM
Hi pt,
Sorry for the late reply, just realized somehow my reply wasn't posted.. And thanks for the clarification.
I indeed didn't use a residuals as an input. The input dataset I used is the result of the bold signal that our algorithm extracted from the original fMRI signal. I wonder whether it's reasonable to use this program to estimate the smoothness on this sort of data. I also sent you in private message a link of google drive that has this dataset.

This is the exact command I used:
Quote

3dFWHMx -detrend 2 -mask task_motor_GM_mask_re+orig.BRIK.gz -dset sub-012_task-stroop_acq-ME5_negDelta_R2_star_valid.nii.gz -acf sub-012_task-motor_negDelta_R2_star >> output
(I also used mask of the grey matter, because we think the signal should have more correlation within the grey matter)

And this is the output I got.
Quote

++ 3dFWHMx: AFNI version=AFNI_21.1.13 (Jun 21 2021) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 42353
*+ WARNING: removed 1978 voxels from mask because they are constant in time
++ detrending start: 7 baseline funcs, 180 time points
+ detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 10.78 mm
** ERROR: calfun[1]=nan --> 0
** ERROR: calfun[2]=nan --> 0
** calfun error: 0.5 -nan -nan
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** calfun error: 0.58882 -nan -nan
** calfun error: 0.0863528 -nan -nan
** calfun error: 0.736319 -nan -nan
** calfun error: 0.00924387 -nan -nan
** calfun error: 0.614497 -nan -nan
** calfun error: 0.652714 -nan -nan
** calfun error: 0.123942 -nan -nan
** calfun error: 0.224788 -nan -nan
** calfun error: 0.881058 -nan -nan
** calfun error: 0.457333 -nan -nan
** calfun error: 0.502193 -nan -nan
** calfun error: 0.899085 -nan -nan
** calfun error: 0.581293 -nan -nan
** calfun error: 0.570047 -nan -nan
** calfun error: 0.20683 -nan -nan
** calfun error: 0.322771 -nan -nan
** calfun error: 0.848737 -nan -nan
** calfun error: 0.547163 -nan -nan
** calfun error: 0.325978 -nan -nan
** calfun error: 0.0441218 -nan -nan
** calfun error: 0.281868 -nan -nan
** calfun error: 0.397327 -nan -nan
** calfun error: 0.080625 -nan -nan
** calfun error: 0.270315 -nan -nan
** calfun error: 0.280573 -nan -nan
** calfun error: 0.881108 -nan -nan
** calfun error: 0.513374 -nan -nan
** calfun error: 0.235958 -nan -nan
** calfun error: 0.446922 -nan -nan
** calfun error: 0.665299 -nan -nan
** calfun error: 0.818381 -nan -nan
** calfun error: 0.823295 -nan -nan
** calfun error: 0.258861 -nan -nan
** calfun error: 0.0432392 -nan -nan
** calfun error: 0.487497 -nan -nan
** calfun error: 0.611275 -nan -nan
** calfun error: 0.536781 -nan -nan
** calfun error: 0.736921 -nan -nan
** calfun error: 0.756628 -nan -nan
** calfun error: 0.303757 -nan -nan
** calfun error: 0.464821 -nan -nan
** calfun error: 0.910727 -nan -nan
** calfun error: 0.626032 -nan -nan
** calfun error: 0.586256 -nan -nan
** calfun error: 0.207976 -nan -nan
** calfun error: 0.223704 -nan -nan
** calfun error: 0.415171 -nan -nan
** calfun error: 0.702904 -nan -nan
** calfun error: 0.587506 -nan -nan
** calfun error: 0.430245 -nan -nan
** calfun error: 0.198843 -nan -nan
** calfun error: 0.414961 -nan -nan
** calfun error: 0.522641 -nan -nan
** calfun error: 0.47101 -nan -nan
** calfun error: 0.543195 -nan -nan
** calfun error: 0.405183 -nan -nan
** calfun error: 0.89818 -nan -nan
** calfun error: 0.299442 -nan -nan
** calfun error: 0.963985 -nan -nan
** calfun error: 0.0712973 -nan -nan
** calfun error: 0.424314 -nan -nan
** calfun error: 0.0809394 -nan -nan
** calfun error: 0.605887 -nan -nan
** calfun error: 0.377424 -nan -nan
** calfun error: 0.375948 -nan -nan
** calfun error: 0.759903 -nan -nan
** calfun error: 0.736869 -nan -nan
** calfun error: 0.609803 -nan -nan
** calfun error: 0.650161 -nan -nan
** calfun error: 0.772724 -nan -nan
** calfun error: 0.144644 -nan -nan
** calfun error: 0.0638747 -nan -nan
** calfun error: 0.238442 -nan -nan
** calfun error: 0.494171 -nan -nan
** calfun error: 0.687252 -nan -nan
** calfun error: 0.62956 -nan -nan
** calfun error: 0.146227 -nan -nan
** calfun error: 0.0604715 -nan -nan
** calfun error: 0.531892 -nan -nan
** calfun error: 0.848379 -nan -nan
** calfun error: 0.775491 -nan -nan
** calfun error: 0.048124 -nan -nan
** calfun error: 0.113735 -nan -nan
** calfun error: 0.396366 -nan -nan
** calfun error: 0.963007 -nan -nan
** calfun error: 0.372676 -nan -nan
** calfun error: 0.686703 -nan -nan
** calfun error: 0.829091 -nan -nan
** calfun error: 0.151971 -nan -nan
** calfun error: 0.975385 -nan -nan
** calfun error: 0.715677 -nan -nan
** calfun error: 0.506699 -nan -nan
** calfun error: 0.0694739 -nan -nan
** calfun error: 0.891099 -nan -nan
** calfun error: 0.0435461 -nan -nan
** calfun error: 0.0347871 -nan -nan
** calfun error: 0.130425 -nan -nan
** calfun error: 0.118446 -nan -nan
** calfun error: 0.219661 -nan -nan
** calfun error: 0.611 -nan -nan
** calfun error: 0.590625 -nan -nan
** calfun error: 0.608408 -nan -nan
** calfun error: 0.265953 -nan -nan
** calfun error: 0.78722 -nan -nan
** calfun error: 0.404545 -nan -nan
** calfun error: 0.0777802 -nan -nan
** calfun error: 0.462125 -nan -nan
** calfun error: 0.457497 -nan -nan
** calfun error: 0.3227 -nan -nan
** calfun error: 0.666429 -nan -nan
** calfun error: 0.0652796 -nan -nan
** calfun error: 0.264879 -nan -nan
** calfun error: 0.459242 -nan -nan
** calfun error: 0.1035 -nan -nan
** calfun error: 0.949271 -nan -nan
** calfun error: 0.131041 -nan -nan
** calfun error: 0.507417 -nan -nan
** calfun error: 0.12789 -nan -nan
** calfun error: 0.0824071 -nan -nan
** calfun error: 0.822152 -nan -nan
** calfun error: 0.105807 -nan -nan
** calfun error: 0.889957 -nan -nan
** calfun error: 0.0260475 -nan -nan
** calfun error: 0.700329 -nan -nan
** calfun error: 0.663898 -nan -nan
** calfun error: 0.33825 -nan -nan
** calfun error: 0.0529286 -nan -nan
** calfun error: 0.572073 -nan -nan
** calfun error: 0.821531 -nan -nan
** calfun error: 0.122197 -nan -nan
** calfun error: 0.295808 -nan -nan
** calfun error: 0.791438 -nan -nan
** calfun error: 0.208397 -nan -nan
** calfun error: 0.778501 -nan -nan
** calfun error: 0.916229 -nan -nan
** calfun error: 0.378687 -nan -nan
** calfun error: 0.472189 -nan -nan
** calfun error: 0.354295 -nan -nan
** calfun error: 0.773147 -nan -nan
** calfun error: 0.49172 -nan -nan
** calfun error: 0.24154 -nan -nan
** calfun error: 0.378748 -nan -nan
** calfun error: 0.597846 -nan -nan
** calfun error: 0.0505326 -nan -nan
** calfun error: 0.22891 -nan -nan
** calfun error: 0.281344 -nan -nan
** calfun error: 0.872457 -nan -nan
** calfun error: 0.199892 -nan -nan
** calfun error: 0.894457 -nan -nan
** calfun error: 0.0239702 -nan -nan
** calfun error: 0.596616 -nan -nan
** calfun error: 0.215822 -nan -nan
** calfun error: 0.768214 -nan -nan
** calfun error: 0.203238 -nan -nan
** calfun error: 0.437941 -nan -nan
** calfun error: 0.579581 -nan -nan
** calfun error: 0.251026 -nan -nan
** calfun error: 0.633517 -nan -nan
** calfun error: 0.707309 -nan -nan
** calfun error: 0.240631 -nan -nan
** calfun error: 0.401416 -nan -nan
** calfun error: 0.169393 -nan -nan
** calfun error: 0.843076 -nan -nan
** calfun error: 0.49657 -nan -nan
** calfun error: 0.343405 -nan -nan
** calfun error: 0.806705 -nan -nan
** calfun error: 0.393859 -nan -nan
** calfun error: 0.243727 -nan -nan
** calfun error: 0.0810603 -nan -nan
** calfun error: 0.563173 -nan -nan
** ERROR: Powell: nothing survived 1st round sad smiley
+ ACF done (0.00 CPU s thus far)
*+ WARNING: Zeroed 29 float errors while writing 1D file sub-012_task-motor_negDelta_R2_star
++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to sub-012_task-motor_negDelta_R2_star
++ 1dplot: AFNI version=AFNI_21.1.13 (Jun 21 2021) [64-bit]
++ Authored by: RWC et al.
pnmtopng: 31 colors found
+ and 1dplot-ed to file sub-012_task-motor_negDelta_R2_star.png

Also, I used this same command except for removing the -detrend option and it ran successfully.

Zixun
Subject Author Posted

-detrend option in 3dFWHMx vs 3dDetrend

Zixun March 30, 2022 02:55AM

Re: -detrend option in 3dFWHMx vs 3dDetrend

ptaylor April 06, 2022 09:56PM

Re: -detrend option in 3dFWHMx vs 3dDetrend

Zixun May 06, 2022 07:23AM

Re: -detrend option in 3dFWHMx vs 3dDetrend

ptaylor May 10, 2022 10:41AM



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