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June 08, 2021 06:01PM
Hi again,
To follow up on this, I think I am noticing a similar error with some other scripts; for example when running the s00.warper script for the FT tutorial dataset on using @SSwarper. It looks like afni on my computer is reporting "WARNING: Bad drive AFNI result from 'SET_PBAR_ALL"..., which is similar to some of the warnings I get when running the afni.proc.py tutorial script. Any idea about what might be causing this issue?

Below is the beginning of the output log for the s00.warper script showing the warning. The script is able to continue with the 3dAllineate function after these warnings.

[Michaels-MacBook-Pro-6:AfniBootcamp/AFNI_data6/FT_analysis] michaelspilka% tcsh s00.warper_MS
++ Starting: @SSwarper v2.5
++ Default OMP_NUM_THREADS is 4
++ Prepare for running @djunct_overlap_check (ver = 0.3)
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./FT/anat_warped/__workdir_olap_On0GkWOz9Vf/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./FT/anat_warped/__workdir_olap_On0GkWOz9Vf/olapch_1_cp_olay.nii
++ 3drefit: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset olapch_0_cp_ulay.nii
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
+ loading and re-writing dataset olapch_0_cp_ulay.nii (/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT/anat_warped/__workdir_olap_On0GkWOz9Vf/olapch_0_cp_ulay.nii in NIFTI storage)
++ 3drefit processed 1 datasets
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 4 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -set_dicom_xyz 0 0 0
\n------------------ start of optionizing ------------------\n
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: ./__tmp_chauf_UirUd8EaFya
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1367.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_UirUd8EaFya/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_UirUd8EaFya/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 1151.000000
++ Dimensions (xyzt): 256 256 175 1
++ (initial) Slice spacing ordered (x,y,z) is: 19 28 28
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=olapch_0_cp_ulay.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_NqAXrjvBo2ExvZCOZ9yjuA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.062029
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_NqAXrjvBo2ExvZCOZ9yjuA+tlrc.BRIK
++ 11468800 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 128 127 86
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :390
[1] 54240

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=3x3:19:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=3x3:28:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 0 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1367.000000 -com SET_FUNC_RANGE 1151.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 128 127 86 -com SAVE_PNG sagittalimage ./img00.sag blowup=2 -com SAVE_PNG coronalimage ./img00.cor blowup=2 -com SAVE_PNG axialimage ./img00.axi blowup=2 -com QUITT ./__tmp_chauf_UirUd8EaFya

+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT/anat_warped/__workdir_olap_On0GkWOz9Vf/__tmp_chauf_UirUd8EaFya*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 0 Reds_and_Blues'
++ Writing one 1536x1536 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./img00.sag.png'
++ Writing one 1120x1536 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./img00.cor.png'
++ Writing one 1120x1536 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./img00.axi.png'

AFNI QUITTs!
\n+* Removing temporary image directory './__tmp_chauf_UirUd8EaFya'.\n
[1] Done Xvfb :390 -screen 0 1024x768x24

++ DONE (good exit)
see: ./img00*

2dcat: No match.
\n+* Removing temporary workdir 'FT/anat_warped/__workdir_olap_On0GkWOz9Vf*'\n

++ DONE! Image output:
FT/anat_warped/init_qc_00_overlap_usrc_obase
Subject Author Posted

APQC output issues Attachments

mjss June 07, 2021 05:35PM

Re: APQC output issues

ptaylor June 07, 2021 05:56PM

Re: APQC output issues

mjss June 07, 2021 08:49PM

Re: APQC output issues

ptaylor June 07, 2021 09:53PM

Re: APQC output issues

mjss June 08, 2021 10:10AM

Re: APQC output issues

mjss June 08, 2021 10:11AM

Re: APQC output issues

mjss June 08, 2021 06:01PM

Re: APQC output issues

ptaylor June 09, 2021 05:02PM

Re: APQC output issues

mjss June 10, 2021 11:49AM

Re: APQC output issues

ptaylor June 10, 2021 06:23PM



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