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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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
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
| June 08, 2021 10:11AM | |
Registered: 2 years ago Posts: 19 |
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%
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%
| Subject | Author | Posted |
|---|---|---|
|
mjss | June 07, 2021 05:35PM |
|
ptaylor | June 07, 2021 05:56PM |
|
mjss | June 07, 2021 08:49PM |
|
ptaylor | June 07, 2021 09:53PM |
|
mjss | June 08, 2021 10:10AM |
|
mjss | June 08, 2021 10:11AM |
|
mjss | June 08, 2021 06:01PM |
|
ptaylor | June 09, 2021 05:02PM |
|
mjss | June 10, 2021 11:49AM |
|
ptaylor | June 10, 2021 06:23PM |
