afni.nimh.nih.gov

Part 2/2:


ERROR: QC_FT.NL/media/qc_11_regr_tsnr_fin.pbar.txt not found!!

++ My command:
@chauffeur_afni -ulay radcor.pb00.tcat/epi.ulay.r01+orig.HEAD -ulay_range 0% 110% -olay radcor.pb00.tcat/radcor.20.r01.corr+orig.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.pbar.jpg -pbar_comm_range ulay is 0th vol of EPI -pbar_comm_thr alpha on -prefix QC_FT.NL/media/qc_12_radcor_rc_tcat_r01 -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: radcor.pb00.tcat/epi.ulay.r01+orig.HEAD
++ Found input file: radcor.pb00.tcat/radcor.20.r01.corr+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_7edwsFLntXj
++ 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, 1764.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_7edwsFLntXj/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_7edwsFLntXj/tmp_olay.nii
++ User-entered function range value value (0.7)
++ Dimensions (xyzt): 80 80 33 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 8 3
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=radcor.pb00.tcat/epi.ulay.r01+orig.HEAD[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_2Xrtf1Tc-8SWKzeuYn5qkA 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 = 0.089757
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_2Xrtf1Tc-8SWKzeuYn5qkA+orig.BRIK
++ 211200 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 40 40 16
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :436
[1] 46895
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_7edwsFLntXj*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:3:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1764.000000 -com SET_FUNC_RANGE 0.7 -com SET_THRESHNEW 0.4 * -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 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_7edwsFLntXj

\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_7edwsFLntXj'.\n

++ DONE (good exit)
see: QC_FT.NL/media/qc_12_radcor_rc_tcat_r01*


ERROR: QC_FT.NL/media/qc_12_radcor_rc_tcat_r01.pbar.txt not found!!

++ My command:
@chauffeur_afni -ulay radcor.pb00.tcat/epi.ulay.r02+orig.HEAD -ulay_range 0% 110% -olay radcor.pb00.tcat/radcor.20.r02.corr+orig.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.pbar.jpg -pbar_comm_range ulay is 0th vol of EPI -pbar_comm_thr alpha on -prefix QC_FT.NL/media/qc_12_radcor_rc_tcat_r02 -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: radcor.pb00.tcat/epi.ulay.r02+orig.HEAD
++ Found input file: radcor.pb00.tcat/radcor.20.r02.corr+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_ItBQGj0tNYB
++ 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, 1770.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_ItBQGj0tNYB/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_ItBQGj0tNYB/tmp_olay.nii
++ User-entered function range value value (0.7)
++ Dimensions (xyzt): 80 80 33 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 8 3
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=radcor.pb00.tcat/epi.ulay.r02+orig.HEAD[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_WfuPHiAk4AaxpBskrBtLrw 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 = 0.080875
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_WfuPHiAk4AaxpBskrBtLrw+orig.BRIK
++ 211200 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 40 40 16
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :192
[1] 47076
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_ItBQGj0tNYB*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:3:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1770.000000 -com SET_FUNC_RANGE 0.7 -com SET_THRESHNEW 0.4 * -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 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_ItBQGj0tNYB

\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_ItBQGj0tNYB'.\n

++ DONE (good exit)
see: QC_FT.NL/media/qc_12_radcor_rc_tcat_r02*


ERROR: QC_FT.NL/media/qc_12_radcor_rc_tcat_r02.pbar.txt not found!!

++ My command:
@chauffeur_afni -ulay radcor.pb00.tcat/epi.ulay.r03+orig.HEAD -ulay_range 0% 110% -olay radcor.pb00.tcat/radcor.20.r03.corr+orig.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.pbar.jpg -pbar_comm_range ulay is 0th vol of EPI -pbar_comm_thr alpha on -prefix QC_FT.NL/media/qc_12_radcor_rc_tcat_r03 -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: radcor.pb00.tcat/epi.ulay.r03+orig.HEAD
++ Found input file: radcor.pb00.tcat/radcor.20.r03.corr+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_aChgTcJ4e2t
++ 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, 1770.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_aChgTcJ4e2t/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_aChgTcJ4e2t/tmp_olay.nii
++ User-entered function range value value (0.7)
++ Dimensions (xyzt): 80 80 33 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 8 3
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=radcor.pb00.tcat/epi.ulay.r03+orig.HEAD[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_4nEdG5snFOWVRTeO43LWYg 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 = 0.098837
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_4nEdG5snFOWVRTeO43LWYg+orig.BRIK
++ 211200 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 40 40 16
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :356
[1] 47257
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_aChgTcJ4e2t*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:3:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1770.000000 -com SET_FUNC_RANGE 0.7 -com SET_THRESHNEW 0.4 * -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 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_aChgTcJ4e2t

\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_aChgTcJ4e2t'.\n

++ DONE (good exit)
see: QC_FT.NL/media/qc_12_radcor_rc_tcat_r03*


ERROR: QC_FT.NL/media/qc_12_radcor_rc_tcat_r03.pbar.txt not found!!

++ My command:
@chauffeur_afni -ulay radcor.pb02.volreg/epi.ulay.r01+tlrc.HEAD -ulay_range 0% 110% -olay radcor.pb02.volreg/radcor.20.r01.corr+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.pbar.jpg -pbar_comm_range ulay is 0th vol of EPI -pbar_comm_thr alpha on -prefix QC_FT.NL/media/qc_13_radcor_rc_volreg_r01 -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: radcor.pb02.volreg/epi.ulay.r01+tlrc.HEAD
++ Found input file: radcor.pb02.volreg/radcor.20.r01.corr+tlrc.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_9o84TPQQN1b
++ 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, 1663.531738]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_9o84TPQQN1b/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_9o84TPQQN1b/tmp_olay.nii
++ User-entered function range value value (0.7)
++ Dimensions (xyzt): 77 92 77 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 10 8
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=radcor.pb02.volreg/epi.ulay.r01+tlrc.HEAD[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_4R7-sVtFgdh5C8Iakt9Y_Q 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 = 0.089694
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_4R7-sVtFgdh5C8Iakt9Y_Q+tlrc.BRIK
++ 545468 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 37 45 38
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :917
[1] 47438
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_9o84TPQQN1b*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1104x924 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.sag.png'
++ Writing one 924x924 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.cor.png'
++ Writing one 924x1104 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:10:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1663.531738 -com SET_FUNC_RANGE 0.7 -com SET_THRESHNEW 0.4 * -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 37 45 38 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_9o84TPQQN1b

\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_9o84TPQQN1b'.\n

++ DONE (good exit)
see: QC_FT.NL/media/qc_13_radcor_rc_volreg_r01*


ERROR: QC_FT.NL/media/qc_13_radcor_rc_volreg_r01.pbar.txt not found!!

++ My command:
@chauffeur_afni -ulay radcor.pb02.volreg/epi.ulay.r02+tlrc.HEAD -ulay_range 0% 110% -olay radcor.pb02.volreg/radcor.20.r02.corr+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.pbar.jpg -pbar_comm_range ulay is 0th vol of EPI -pbar_comm_thr alpha on -prefix QC_FT.NL/media/qc_13_radcor_rc_volreg_r02 -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: radcor.pb02.volreg/epi.ulay.r02+tlrc.HEAD
++ Found input file: radcor.pb02.volreg/radcor.20.r02.corr+tlrc.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_CYIMxQW8jS2
++ 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, 1664.045166]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_CYIMxQW8jS2/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_CYIMxQW8jS2/tmp_olay.nii
++ User-entered function range value value (0.7)
++ Dimensions (xyzt): 77 92 77 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 10 8
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=radcor.pb02.volreg/epi.ulay.r02+tlrc.HEAD[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_foPj756mcYYU04qVAH1yJA 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 = 0.081004
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_foPj756mcYYU04qVAH1yJA+tlrc.BRIK
++ 545468 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 37 45 38
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :849
[1] 47619
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_CYIMxQW8jS2*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1104x924 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.sag.png'
++ Writing one 924x924 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.cor.png'
++ Writing one 924x1104 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:10:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1664.045166 -com SET_FUNC_RANGE 0.7 -com SET_THRESHNEW 0.4 * -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 37 45 38 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_CYIMxQW8jS2

\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_CYIMxQW8jS2'.\n

++ DONE (good exit)
see: QC_FT.NL/media/qc_13_radcor_rc_volreg_r02*


ERROR: QC_FT.NL/media/qc_13_radcor_rc_volreg_r02.pbar.txt not found!!

++ My command:
@chauffeur_afni -ulay radcor.pb02.volreg/epi.ulay.r03+tlrc.HEAD -ulay_range 0% 110% -olay radcor.pb02.volreg/radcor.20.r03.corr+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.pbar.jpg -pbar_comm_range ulay is 0th vol of EPI -pbar_comm_thr alpha on -prefix QC_FT.NL/media/qc_13_radcor_rc_volreg_r03 -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: radcor.pb02.volreg/epi.ulay.r03+tlrc.HEAD
++ Found input file: radcor.pb02.volreg/radcor.20.r03.corr+tlrc.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_uMjbOyUtKHi
++ 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, 1669.748535]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_uMjbOyUtKHi/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_uMjbOyUtKHi/tmp_olay.nii
++ User-entered function range value value (0.7)
++ Dimensions (xyzt): 77 92 77 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 10 8
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=radcor.pb02.volreg/epi.ulay.r03+tlrc.HEAD[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_VB5HyfpsGdXziBcGlL_ACQ 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 = 0.096995
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_VB5HyfpsGdXziBcGlL_ACQ+tlrc.BRIK
++ 545468 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 37 45 38
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :947
[1] 47800
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_uMjbOyUtKHi*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1104x924 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.sag.png'
++ Writing one 924x924 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.cor.png'
++ Writing one 924x1104 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:10:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1669.748535 -com SET_FUNC_RANGE 0.7 -com SET_THRESHNEW 0.4 * -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 37 45 38 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_uMjbOyUtKHi

\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_uMjbOyUtKHi'.\n

++ DONE (good exit)
see: QC_FT.NL/media/qc_13_radcor_rc_volreg_r03*


ERROR: QC_FT.NL/media/qc_13_radcor_rc_volreg_r03.pbar.txt not found!!

++ Check for corr matrix warnings in: QC_FT.NL/media/qc_14_warns_xmat.dat
++ Check for censor fraction warnings (general): QC_FT.NL/media/qc_15_warns_cen_total.dat
++ Check for censor fraction warnings (per stim): QC_FT.NL/media/qc_16_warns_cen_stim.dat
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (vr_base_min_outlier_ts_ns+orig) to workdir
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_tTjzJAHEsRe/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_tTjzJAHEsRe/eac_0_cp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__workdir_EAC_tTjzJAHEsRe/eac_0_cp.nii
++ Base dataset: (not given)
++ Loading datasets into memory
+ -cmass x y z shifts = 0.000 0.000 0.000
+ shift search range is +/- = 69.737 69.737 30.816
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset QC_FT.NL/media/__workdir_EAC_tTjzJAHEsRe/eac_1_grid2olay.nii
++ 3dAllineate: total CPU time = 15.6 sec Elapsed = 4.5
++ ###########################################################
++ Output dataset ./eac_2_ulay_shrp.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 ./QC_FT.NL/media/__workdir_EAC_tTjzJAHEsRe/eac_3_cp.nii
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_3_cp.nii
++ Forming automask
+ Fixed clip level = 445.235809
+ Used gradual clip level = 436.239655 .. 450.102570
+ Number voxels above clip level = 1514426
+ Clustering voxels ...
+ Largest cluster has 1514385 voxels
+ Clustering voxels ...
+ Largest cluster has 1508400 voxels
+ Filled 21125 voxels in small holes; now have 1529525 voxels
+ Filled 62528 voxels in large holes; now have 1592053 voxels
+ Clustering voxels ...
+ Largest cluster has 1592002 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 3199178 voxels
+ Mask now has 1592422 voxels
++ 1592422 voxels in the mask [out of 4791600: 33.23%]
++ first 40 x-planes are zero [from R]
++ last 41 x-planes are zero [from L]
++ first 26 y-planes are zero [from A]
++ last 2 y-planes are zero [from P]
++ first 0 z-planes are zero [from I]
++ last 0 z-planes are zero [from S]
++ Output dataset ./eac_4_mask.nii
++ CPU time = 0.870000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Output dataset ./eac_5_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_2_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_6_edgy.nii -ulay_range_nz 2% 98% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 19.762463 -opacity 9 -prefix ../qc_18_warns_flip_0 -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: eac_2_ulay_shrp.nii
++ Found input file: eac_6_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_YpMMtefPIBO
++ 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, 1788.184326]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_YpMMtefPIBO/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_YpMMtefPIBO/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 242.499481
++ Dimensions (xyzt): 220 220 99 1
++ (initial) Slice spacing ordered (x,y,z) is: 24 24 11
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_2_ulay_shrp.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_volXC9dbH1Ln91YLlWWpVg 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 = 0.101190
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_volXC9dbH1Ln91YLlWWpVg+orig.BRIK
++ 4791600 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 110 110 49
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :982
[1] 48037
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_YpMMtefPIBO*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1320x594 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_18_warns_flip_0.sag.png'
++ Writing one 1320x594 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_18_warns_flip_0.cor.png'
++ Writing one 1320x1320 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_18_warns_flip_0.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:24:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:11:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1788.184326 -com SET_FUNC_RANGE 242.499481 -com SET_THRESHNEW 19.762463 * -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 110 110 49 -com SAVE_PNG sagittalimage ../qc_18_warns_flip_0.sag blowup=2 -com SAVE_PNG coronalimage ../qc_18_warns_flip_0.cor blowup=2 -com SAVE_PNG axialimage ../qc_18_warns_flip_0.axi blowup=2 -com QUITT ../__tmp_chauf_YpMMtefPIBO

\n+* Removing temporary image directory '../__tmp_chauf_YpMMtefPIBO'.\n

++ DONE (good exit)
see: ../qc_18_warns_flip_0*

\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_tTjzJAHEsRe*'\n

++ DONE! Image output:
QC_FT.NL/media/qc_18_warns_flip_0

++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (vr_base_min_outlier_ts_ns+orig) to workdir
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_xKwxBiHOAU9/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_xKwxBiHOAU9/eac_0_cp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__workdir_EAC_xKwxBiHOAU9/eac_0_cp.nii
++ Base dataset: (not given)
++ Loading datasets into memory
+ -cmass x y z shifts = 0.000 0.000 0.000
+ shift search range is +/- = 69.737 69.737 30.816
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset QC_FT.NL/media/__workdir_EAC_xKwxBiHOAU9/eac_1_grid2olay.nii
++ 3dAllineate: total CPU time = 15.7 sec Elapsed = 4.5
++ ###########################################################
++ Output dataset ./eac_2_ulay_shrp.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 ./QC_FT.NL/media/__workdir_EAC_xKwxBiHOAU9/eac_3_cp.nii
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_3_cp.nii
++ Forming automask
+ Fixed clip level = 445.530762
+ Used gradual clip level = 439.041718 .. 448.922729
+ Number voxels above clip level = 1606824
+ Clustering voxels ...
+ Largest cluster has 1606723 voxels
+ Clustering voxels ...
+ Largest cluster has 1600724 voxels
+ Filled 22118 voxels in small holes; now have 1622842 voxels
+ Filled 65973 voxels in large holes; now have 1688815 voxels
+ Clustering voxels ...
+ Largest cluster has 1688773 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 3102432 voxels
+ Mask now has 1689168 voxels
++ 1689168 voxels in the mask [out of 4791600: 35.25%]
++ first 37 x-planes are zero [from R]
++ last 41 x-planes are zero [from L]
++ first 23 y-planes are zero [from A]
++ last 0 y-planes are zero [from P]
++ first 0 z-planes are zero [from I]
++ last 0 z-planes are zero [from S]
++ Output dataset ./eac_4_mask.nii
++ CPU time = 0.850000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Output dataset ./eac_5_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_2_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_6_edgy.nii -ulay_range_nz 2% 98% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 19.288048 -opacity 9 -prefix ../qc_18_warns_flip_1 -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: eac_2_ulay_shrp.nii
++ Found input file: eac_6_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_ftniQ0rM1WW
++ 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, 1788.184326]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_ftniQ0rM1WW/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_ftniQ0rM1WW/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 243.338577
++ Dimensions (xyzt): 220 220 99 1
++ (initial) Slice spacing ordered (x,y,z) is: 24 24 11
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_2_ulay_shrp.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_YodVaMIoBUKO9fhuh5EOuQ 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 = 0.101190
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_YodVaMIoBUKO9fhuh5EOuQ+orig.BRIK
++ 4791600 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 110 110 49
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :472
[1] 48247
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_ftniQ0rM1WW*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1320x594 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_18_warns_flip_1.sag.png'
++ Writing one 1320x594 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_18_warns_flip_1.cor.png'
++ Writing one 1320x1320 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_18_warns_flip_1.axi.png'

AFNI QUITTs!

+++ 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=9 mont=3x3:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:24:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:11:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1788.184326 -com SET_FUNC_RANGE 243.338577 -com SET_THRESHNEW 19.288048 * -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 110 110 49 -com SAVE_PNG sagittalimage ../qc_18_warns_flip_1.sag blowup=2 -com SAVE_PNG coronalimage ../qc_18_warns_flip_1.cor blowup=2 -com SAVE_PNG axialimage ../qc_18_warns_flip_1.axi blowup=2 -com QUITT ../__tmp_chauf_ftniQ0rM1WW

\n+* Removing temporary image directory '../__tmp_chauf_ftniQ0rM1WW'.\n
[1] Done Xvfb :472 -screen 0 1024x768x24

++ DONE (good exit)
see: ../qc_18_warns_flip_1*

\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_xKwxBiHOAU9*'\n

++ DONE! Image output:
QC_FT.NL/media/qc_18_warns_flip_1

++ Check basic summary quants from proc in: QC_FT.NL/media/qc_19_qsumm_ssrev.dat


# +++++++++++ Check output of @ss_review_basic +++++++++++ #


subject ID : FT.NL
AFNI version : AFNI_21.1.02
AFNI package : macos_10.12_local
TR : 2.0
TRs removed (per run) : 2
num stim classes provided : 2
final anatomy dset : anat_final.FT.NL+tlrc.HEAD
final stats dset : stats.FT.NL+tlrc.HEAD
final voxel resolution : 2.500000 2.500000 2.500000

motion limit : 0.3
num TRs above mot limit : 3
average motion (per TR) : 0.0753814
average censored motion : 0.0690134
max motion displacement : 1.66098
max censored displacement : 1.03121
outlier limit : 0.05
average outlier frac (TR) : 0.00276734
num TRs above out limit : 2
flip guess : NO_FLIP

num runs found : 3
num TRs per run : 150 150 150
num TRs per run (applied) : 146 148 150
num TRs per run (censored): 4 2 0
fraction censored per run : 0.0266667 0.0133333 0
TRs total (uncensored) : 450
TRs total : 444
degrees of freedom used : 32
degrees of freedom left : 412

TRs censored : 6
censor fraction : 0.013333
num regs of interest : 2
num TRs per stim (orig) : 240 239
num TRs censored per stim : 6 0
fraction TRs censored : 0.025 0.000
ave mot per sresp (orig) : 0.078214 0.071134
ave mot per sresp (cens) : 0.066285 0.071134

TSNR average : 201.333
global correlation (GCOR) : 0.0471121
anat/EPI mask Dice coef : 0.828442
anat/templ mask Dice coef : 0.842005
maximum F-stat (masked) : 970.802
blur estimates (ACF) : 0.730285 3.11569 10.8688
blur estimates (FWHM) : 0 0 0


Traceback (most recent call last):
File "/Users/michaelspilka/abin/apqc_make_html.py", line 193, in <module>
AAII = lah.read_descrip_json(img_json)
File "/Users/michaelspilka/abin/afnipy/lib_apqc_html.py", line 1746, in read_descrip_json
ainfo.set_all_from_dict(ddd) # set everything in this obj that we can
File "/Users/michaelspilka/abin/afnipy/lib_apqc_html.py", line 642, in set_all_from_dict
self.add_subtext(DICT)
File "/Users/michaelspilka/abin/afnipy/lib_apqc_html.py", line 625, in add_subtext
xx = parse_apqc_text_fields(DICT['subtext'])
File "/Users/michaelspilka/abin/afnipy/lib_apqc_html.py", line 517, in parse_apqc_text_fields
sspbar = make_inline_pbar_str(ss)
File "/Users/michaelspilka/abin/afnipy/lib_apqc_html.py", line 546, in make_inline_pbar_str
with open(fname_json, 'r') as fff:
FileNotFoundError: [Errno 2] No such file or directory: 'media/qc_06_mot_grayplot.pbar.json'
[Michaels-MacBook-Pro-6:AFNI_data6/FT_analysis/FT.NL.results] michaelspilka%