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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 10:10AM | |
Registered: 3 years ago Posts: 19 |
Thank you for your help with this. I updated my afni binaries but unfortunately I'm still encountering the same problems. Here is the log from the redo_apqc script (copied in 2 parts because of the message character limit):
1/2:
[Michaels-MacBook-Pro-6:AFNI_data6/FT_analysis/FT.NL.results] michaelspilka% tcsh redo_apqc.tcsh
++ REDOing APQC
++ Going to re-run APQC in this dir only: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results
++ Found 41 files for QCing.
++ Done making (executable) script to generate HTML QC:
./@ss_review_html
*+ Found main dset (template): /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ My command:
@chauffeur_afni -ulay vr_base_min_outlier+orig.HEAD -olay vr_base_min_outlier+orig.HEAD -ulay_range_nz 0 1751.000000 -func_range 1751.000000 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim QC_FT.NL/media/qc_00_vorig_EPI.pbar.jpg -pbar_comm_range 98%ile in vol -pbar_for dset -prefix QC_FT.NL/media/qc_00_vorig_EPI -save_ftype JPEG -blowup 4 -opacity 9 -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: vr_base_min_outlier+orig.HEAD
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
++ Converted 0 to labels
++ Final subbrick indices: -1 -1 -1
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1751.000000]
++ 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_bbULaIX34j9/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_bbULaIX34j9/tmp_olay.nii
++ User-entered function range value value (1751.000000)
++ 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]=vr_base_min_outlier+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_6sTfbGnj_VZMWRtARIWKNA 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 = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_6sTfbGnj_VZMWRtARIWKNA+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 :611
[1] 45065
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_bbULaIX34j9*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean gray_scale'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.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 gray_scale -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 1751.000000 -com SET_FUNC_RANGE 1751.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_00_vorig_EPI.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_00_vorig_EPI.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_00_vorig_EPI.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_bbULaIX34j9'.\n
++ DONE (good exit)
see: QC_FT.NL/media/qc_00_vorig_EPI*
ERROR: QC_FT.NL/media/qc_00_vorig_EPI.pbar.txt not found!!
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) 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_Zafa5dlo38B/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_Zafa5dlo38B/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_Zafa5dlo38B/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 +/- = 60.990 73.028 60.990
++ 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_Zafa5dlo38B/eac_1_grid2olay.nii
++ 3dAllineate: total CPU time = 28.1 sec Elapsed = 8.6
++ ###########################################################
++ 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_Zafa5dlo38B/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 = 457.476471
+ Used gradual clip level = 444.055969 .. 462.343231
+ Number voxels above clip level = 1751345
+ Clustering voxels ...
+ Largest cluster has 1751228 voxels
+ Clustering voxels ...
+ Largest cluster has 1735652 voxels
+ Filled 25607 voxels in small holes; now have 1761259 voxels
+ Filled 88085 voxels in large holes; now have 1849344 voxels
+ Clustering voxels ...
+ Largest cluster has 1849333 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6679560 voxels
+ Mask now has 1850461 voxels
++ 1850461 voxels in the mask [out of 8530021: 21.69%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 25 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 5 z-planes are zero [from I]
++ last 31 z-planes are zero [from S]
++ Output dataset ./eac_4_mask.nii
++ CPU time = 1.870000 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 17.745312 -opacity 9 -prefix ../qc_01_ve2a_epi2anat -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_mB1CFMIc4np
++ 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, 1683.303589]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_mB1CFMIc4np/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_mB1CFMIc4np/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 245.202560
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 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_XGAxa3qRzo9hHcisRjjjiw 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 = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_XGAxa3qRzo9hHcisRjjjiw+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :225
[1] 45280
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_mB1CFMIc4np*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0: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 1683.303589 -com SET_FUNC_RANGE 245.202560 -com SET_THRESHNEW 17.745312 * -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 95 114 96 -com SAVE_PNG sagittalimage ../qc_01_ve2a_epi2anat.sag blowup=2 -com SAVE_PNG coronalimage ../qc_01_ve2a_epi2anat.cor blowup=2 -com SAVE_PNG axialimage ../qc_01_ve2a_epi2anat.axi blowup=2 -com QUITT ../__tmp_chauf_mB1CFMIc4np
\n+* Removing temporary image directory '../__tmp_chauf_mB1CFMIc4np'.\n
++ DONE (good exit)
see: ../qc_01_ve2a_epi2anat*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_01_ve2a_epi2anat
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) 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_JATZ4xJK2Wf/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_JATZ4xJK2Wf/eac_0_cp.nii
++ Output dataset ./eac_1_ulay_shrp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets into memory
*+ WARNING: -1D*_apply '1D: 12@0'': 1 isn't enough rows for source dataset -- last row will repeat
+ -cmass x y z shifts = -0.008 -0.005 0.029
+ shift search range is +/- = 61.632 73.188 61.632
++ OpenMP thread count = 4
++ ========== Applying transformation to 5 sub-bricks ==========
volume 0..1*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #1
..2*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #2
..3*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #3
..4
*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #4
++ Output dataset QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/eac_2_res.nii
++ 3dAllineate: total CPU time = 5.0 sec Elapsed = 4.4
++ ###########################################################
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_2_res.nii
++ Forming automask
+ Fixed clip level = 866.280640
+ Used gradual clip level = 839.463562 .. 889.332031
+ Number voxels above clip level = 1839751
+ Clustering voxels ...
+ Largest cluster has 1839749 voxels
+ Clustering voxels ...
+ Largest cluster has 1839644 voxels
+ Filled 2255 voxels in small holes; now have 1841899 voxels
+ Filled 40056 voxels in large holes; now have 1881955 voxels
+ Clustering voxels ...
+ Largest cluster has 1881949 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6644410 voxels
+ Mask now has 1885611 voxels
++ 1885611 voxels in the mask [out of 8530021: 22.11%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 24 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 6 z-planes are zero [from I]
++ last 32 z-planes are zero [from S]
++ Output dataset ./eac_3_mask.nii
++ CPU time = 2.850000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
*+ WARNING: Only processing sub-brick #0
++ Output dataset ./eac_4_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_1_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_5_edgy.nii -ulay_range 0% 120% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 22.371048 -opacity 9 -prefix ../qc_02_va2t_anat2temp -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_1_ulay_shrp.nii
++ Found input file: eac_5_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_kCrlzLJwrjM
++ 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, 1127.647339]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_kCrlzLJwrjM/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_kCrlzLJwrjM/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 344.516327
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_1_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_mMcw3A-Fv9qWTkpJrJtZFw 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 = 0.172907
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_mMcw3A-Fv9qWTkpJrJtZFw+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :623
[1] 45495
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_kCrlzLJwrjM*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0: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 1127.647339 -com SET_FUNC_RANGE 344.516327 -com SET_THRESHNEW 22.371048 * -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 95 114 96 -com SAVE_PNG sagittalimage ../qc_02_va2t_anat2temp.sag blowup=2 -com SAVE_PNG coronalimage ../qc_02_va2t_anat2temp.cor blowup=2 -com SAVE_PNG axialimage ../qc_02_va2t_anat2temp.axi blowup=2 -com QUITT ../__tmp_chauf_kCrlzLJwrjM
\n+* Removing temporary image directory '../__tmp_chauf_kCrlzLJwrjM'.\n
[1] Done Xvfb :623 -screen 0 1024x768x24
++ DONE (good exit)
see: ../qc_02_va2t_anat2temp*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_02_va2t_anat2temp
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay stats.FT.NL+tlrc.HEAD -cbar Plasma -pbar_posonly -ulay_range 0% 120% -func_range 243.879257 -thr_olay 23.285336 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.jpg -pbar_comm_range 99%ile in mask -pbar_comm_thr 90%ile in mask, alpha+boxed on -prefix QC_FT.NL/media/qc_03_vstat_Full_Fstat -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: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: stats.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
++ 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, 1059.000000]
++ 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_T9OLFqLeRxL/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_T9OLFqLeRxL/tmp_olay.nii
++ User-entered function range value value (243.879257)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[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_iIEqlfFAe1ogWogEqzqX4w 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 = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_iIEqlfFAe1ogWogEqzqX4w+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :35
[1] 45687
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean Plasma'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean Plasma -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 243.879257 -com SET_THRESHNEW 23.285336 * -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 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL'.\n
[1] Done Xvfb :35 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_03_vstat_Full_Fstat*
ERROR: QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.txt not found!!
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
++ Done! Figure created:
QC_FT.NL/media/qc_04_mot_enormoutlr.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: dfile_rall.1D: 6 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
++ Done! Figure created:
QC_FT.NL/media/qc_05_mot_VR6.jpg
++ 3dGrayplot: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
+ Loading dataset ./errts.FT.NL+tlrc.HEAD
+ Number of voxels in mask = 93399
+ 3dGrayplot: Elapsed = 30.1 s
++ My command:
@chauffeur_afni -ulay mask_epi_anat.FT.NL+tlrc.HEAD -olay mask_epi_anat.FT.NL+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar gray_scale -func_range 3.29 -blowup 1 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_06_mot_grayplot.pbar.jpg -pbar_comm_range for normal distr, bounds of 0.001 prob tail -prefix __tmp_ZXCV_img -save_ftype JPEG -montx 1 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Using blowup factor: 1
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_FeFJxDdgsc6
++ 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, 1.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_FeFJxDdgsc6/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_FeFJxDdgsc6/tmp_olay.nii
++ User-entered function range value value (3.29)
++ 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]=mask_epi_anat.FT.NL+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_dk6pqsxyELKZhRcoPE7y_g 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: no scale factor
++ Computing output statistics
++ 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 :470
[1] 45908
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/__tmp_chauf_FeFJxDdgsc6*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean gray_scale'
++ Writing one 276x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.sag.png'
++ Writing one 231x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.cor.png'
++ Writing one 231x276 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.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 gray_scale -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 3.29 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 37 45 38 -com SAVE_PNG sagittalimage ./__tmp_ZXCV_img.sag blowup=1 -com SAVE_PNG coronalimage ./__tmp_ZXCV_img.cor blowup=1 -com SAVE_PNG axialimage ./__tmp_ZXCV_img.axi blowup=1 -com QUITT ./__tmp_chauf_FeFJxDdgsc6
\n+* Removing temporary image directory './__tmp_chauf_FeFJxDdgsc6'.\n
++ DONE (good exit)
see: ./__tmp_ZXCV_img*
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
*+ No ylabels entered
*+ No input x-axis; making values based on length of data: [0..449]
++ Will scale each time series by censor_hline
++ Apply scale: 3.3333333333333335
++ Apply scale: 20.0
++ Will apply same y-axis range '[0.0, 3.0]' to all dsets
++ Plotting:
++ Plotting:
++ Done! Figure created:
__tmp_img_enorm.jpg
\n+* Removing temporary files '__tmp_gluing*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_06_mot_grayplot.jpg
rm: No match.
ERROR: QC_FT.NL/media/qc_06_mot_grayplot.pbar.txt not found!!
++ FOR: sum_ideal.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: regressor sum
++ Done! Figure created:
QC_FT.NL/media/qc_07_regr_ideal.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: X.stim.xmat.1D: 2 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: aud#0
++ Plotting: vis#0
++ Done! Figure created:
QC_FT.NL/media/qc_08_regr_stims.jpg
++ Check summary of degrees of freedom in: QC_FT.NL/media/qc_09_regr_df.dat
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay corr_brain+tlrc.HEAD -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_10_regr_corr_errts.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_FT.NL/media/qc_10_regr_corr_errts -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: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: corr_brain+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
++ 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, 1059.000000]
++ 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_BLZD0SdnOo7/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_BLZD0SdnOo7/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[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_s51H8xERyU7XnMhwQSAAPQ 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 = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_s51H8xERyU7XnMhwQSAAPQ+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :948
[1] 46169
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0: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 1059.000000 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -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 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_10_regr_corr_errts.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_10_regr_corr_errts.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_10_regr_corr_errts.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7'.\n
[1] Done Xvfb :948 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_10_regr_corr_errts*
ERROR: QC_FT.NL/media/qc_10_regr_corr_errts.pbar.txt not found!!
++ Prepare for running adjunct_apqc_tsnr_general (ver = 1.1)
++ MODE: 10
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay TSNR.FT.NL+tlrc.HEAD -ulay_range 0% 120% -func_range 322 -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -set_subbricks 0 0 0 -pbar_posonly -blowup 2 -cbar 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -cbar_ncolors 8 -cbar_topval EMPTY -opacity 4 -olay_alpha No -olay_boxed No -thr_olay 0 -pbar_saveim QC_FT.NL/media/qc_11_regr_tsnr_fin.pbar -pbar_comm_range 95%ile in mask -pbar_comm_gen cbar: hot color range (5-95%ile TSNR in mask): 84 - 322 -prefix QC_FT.NL/media/qc_11_regr_tsnr_fin -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: TSNR.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
++ 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, 1059.000000]
++ 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_ac7ziXX1U2B/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_ac7ziXX1U2B/tmp_olay.nii
++ User-entered function range value value (322)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[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_N0u5gfOjMnNaKFqHj1TT0Q 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 = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_N0u5gfOjMnNaKFqHj1TT0Q+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :638
[1] 46712
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.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=4 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 322 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_11_regr_tsnr_fin.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B'.\n
[1] Done Xvfb :638 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_11_regr_tsnr_fin*
1/2:
[Michaels-MacBook-Pro-6:AFNI_data6/FT_analysis/FT.NL.results] michaelspilka% tcsh redo_apqc.tcsh
++ REDOing APQC
++ Going to re-run APQC in this dir only: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results
++ Found 41 files for QCing.
++ Done making (executable) script to generate HTML QC:
./@ss_review_html
*+ Found main dset (template): /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ My command:
@chauffeur_afni -ulay vr_base_min_outlier+orig.HEAD -olay vr_base_min_outlier+orig.HEAD -ulay_range_nz 0 1751.000000 -func_range 1751.000000 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim QC_FT.NL/media/qc_00_vorig_EPI.pbar.jpg -pbar_comm_range 98%ile in vol -pbar_for dset -prefix QC_FT.NL/media/qc_00_vorig_EPI -save_ftype JPEG -blowup 4 -opacity 9 -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: vr_base_min_outlier+orig.HEAD
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
++ Converted 0 to labels
++ Final subbrick indices: -1 -1 -1
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1751.000000]
++ 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_bbULaIX34j9/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_bbULaIX34j9/tmp_olay.nii
++ User-entered function range value value (1751.000000)
++ 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]=vr_base_min_outlier+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_6sTfbGnj_VZMWRtARIWKNA 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 = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_6sTfbGnj_VZMWRtARIWKNA+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 :611
[1] 45065
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_bbULaIX34j9*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean gray_scale'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.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 gray_scale -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 1751.000000 -com SET_FUNC_RANGE 1751.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_00_vorig_EPI.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_00_vorig_EPI.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_00_vorig_EPI.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_bbULaIX34j9'.\n
++ DONE (good exit)
see: QC_FT.NL/media/qc_00_vorig_EPI*
ERROR: QC_FT.NL/media/qc_00_vorig_EPI.pbar.txt not found!!
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) 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_Zafa5dlo38B/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_Zafa5dlo38B/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_Zafa5dlo38B/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 +/- = 60.990 73.028 60.990
++ 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_Zafa5dlo38B/eac_1_grid2olay.nii
++ 3dAllineate: total CPU time = 28.1 sec Elapsed = 8.6
++ ###########################################################
++ 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_Zafa5dlo38B/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 = 457.476471
+ Used gradual clip level = 444.055969 .. 462.343231
+ Number voxels above clip level = 1751345
+ Clustering voxels ...
+ Largest cluster has 1751228 voxels
+ Clustering voxels ...
+ Largest cluster has 1735652 voxels
+ Filled 25607 voxels in small holes; now have 1761259 voxels
+ Filled 88085 voxels in large holes; now have 1849344 voxels
+ Clustering voxels ...
+ Largest cluster has 1849333 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6679560 voxels
+ Mask now has 1850461 voxels
++ 1850461 voxels in the mask [out of 8530021: 21.69%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 25 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 5 z-planes are zero [from I]
++ last 31 z-planes are zero [from S]
++ Output dataset ./eac_4_mask.nii
++ CPU time = 1.870000 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 17.745312 -opacity 9 -prefix ../qc_01_ve2a_epi2anat -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_mB1CFMIc4np
++ 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, 1683.303589]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_mB1CFMIc4np/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_mB1CFMIc4np/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 245.202560
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 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_XGAxa3qRzo9hHcisRjjjiw 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 = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_XGAxa3qRzo9hHcisRjjjiw+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :225
[1] 45280
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_mB1CFMIc4np*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0: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 1683.303589 -com SET_FUNC_RANGE 245.202560 -com SET_THRESHNEW 17.745312 * -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 95 114 96 -com SAVE_PNG sagittalimage ../qc_01_ve2a_epi2anat.sag blowup=2 -com SAVE_PNG coronalimage ../qc_01_ve2a_epi2anat.cor blowup=2 -com SAVE_PNG axialimage ../qc_01_ve2a_epi2anat.axi blowup=2 -com QUITT ../__tmp_chauf_mB1CFMIc4np
\n+* Removing temporary image directory '../__tmp_chauf_mB1CFMIc4np'.\n
++ DONE (good exit)
see: ../qc_01_ve2a_epi2anat*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_01_ve2a_epi2anat
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) 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_JATZ4xJK2Wf/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_JATZ4xJK2Wf/eac_0_cp.nii
++ Output dataset ./eac_1_ulay_shrp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets into memory
*+ WARNING: -1D*_apply '1D: 12@0'': 1 isn't enough rows for source dataset -- last row will repeat
+ -cmass x y z shifts = -0.008 -0.005 0.029
+ shift search range is +/- = 61.632 73.188 61.632
++ OpenMP thread count = 4
++ ========== Applying transformation to 5 sub-bricks ==========
volume 0..1*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #1
..2*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #2
..3*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #3
..4
*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #4
++ Output dataset QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/eac_2_res.nii
++ 3dAllineate: total CPU time = 5.0 sec Elapsed = 4.4
++ ###########################################################
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_2_res.nii
++ Forming automask
+ Fixed clip level = 866.280640
+ Used gradual clip level = 839.463562 .. 889.332031
+ Number voxels above clip level = 1839751
+ Clustering voxels ...
+ Largest cluster has 1839749 voxels
+ Clustering voxels ...
+ Largest cluster has 1839644 voxels
+ Filled 2255 voxels in small holes; now have 1841899 voxels
+ Filled 40056 voxels in large holes; now have 1881955 voxels
+ Clustering voxels ...
+ Largest cluster has 1881949 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6644410 voxels
+ Mask now has 1885611 voxels
++ 1885611 voxels in the mask [out of 8530021: 22.11%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 24 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 6 z-planes are zero [from I]
++ last 32 z-planes are zero [from S]
++ Output dataset ./eac_3_mask.nii
++ CPU time = 2.850000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
*+ WARNING: Only processing sub-brick #0
++ Output dataset ./eac_4_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_1_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_5_edgy.nii -ulay_range 0% 120% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 22.371048 -opacity 9 -prefix ../qc_02_va2t_anat2temp -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_1_ulay_shrp.nii
++ Found input file: eac_5_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_kCrlzLJwrjM
++ 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, 1127.647339]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_kCrlzLJwrjM/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_kCrlzLJwrjM/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 344.516327
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_1_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_mMcw3A-Fv9qWTkpJrJtZFw 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 = 0.172907
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_mMcw3A-Fv9qWTkpJrJtZFw+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :623
[1] 45495
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_kCrlzLJwrjM*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0: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 1127.647339 -com SET_FUNC_RANGE 344.516327 -com SET_THRESHNEW 22.371048 * -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 95 114 96 -com SAVE_PNG sagittalimage ../qc_02_va2t_anat2temp.sag blowup=2 -com SAVE_PNG coronalimage ../qc_02_va2t_anat2temp.cor blowup=2 -com SAVE_PNG axialimage ../qc_02_va2t_anat2temp.axi blowup=2 -com QUITT ../__tmp_chauf_kCrlzLJwrjM
\n+* Removing temporary image directory '../__tmp_chauf_kCrlzLJwrjM'.\n
[1] Done Xvfb :623 -screen 0 1024x768x24
++ DONE (good exit)
see: ../qc_02_va2t_anat2temp*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_02_va2t_anat2temp
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay stats.FT.NL+tlrc.HEAD -cbar Plasma -pbar_posonly -ulay_range 0% 120% -func_range 243.879257 -thr_olay 23.285336 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.jpg -pbar_comm_range 99%ile in mask -pbar_comm_thr 90%ile in mask, alpha+boxed on -prefix QC_FT.NL/media/qc_03_vstat_Full_Fstat -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: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: stats.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
++ 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, 1059.000000]
++ 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_T9OLFqLeRxL/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_T9OLFqLeRxL/tmp_olay.nii
++ User-entered function range value value (243.879257)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[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_iIEqlfFAe1ogWogEqzqX4w 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 = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_iIEqlfFAe1ogWogEqzqX4w+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :35
[1] 45687
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean Plasma'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean Plasma -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 243.879257 -com SET_THRESHNEW 23.285336 * -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 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL'.\n
[1] Done Xvfb :35 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_03_vstat_Full_Fstat*
ERROR: QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.txt not found!!
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
++ Done! Figure created:
QC_FT.NL/media/qc_04_mot_enormoutlr.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: dfile_rall.1D: 6 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
++ Done! Figure created:
QC_FT.NL/media/qc_05_mot_VR6.jpg
++ 3dGrayplot: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
+ Loading dataset ./errts.FT.NL+tlrc.HEAD
+ Number of voxels in mask = 93399
+ 3dGrayplot: Elapsed = 30.1 s
++ My command:
@chauffeur_afni -ulay mask_epi_anat.FT.NL+tlrc.HEAD -olay mask_epi_anat.FT.NL+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar gray_scale -func_range 3.29 -blowup 1 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_06_mot_grayplot.pbar.jpg -pbar_comm_range for normal distr, bounds of 0.001 prob tail -prefix __tmp_ZXCV_img -save_ftype JPEG -montx 1 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Using blowup factor: 1
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_FeFJxDdgsc6
++ 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, 1.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_FeFJxDdgsc6/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_FeFJxDdgsc6/tmp_olay.nii
++ User-entered function range value value (3.29)
++ 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]=mask_epi_anat.FT.NL+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_dk6pqsxyELKZhRcoPE7y_g 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: no scale factor
++ Computing output statistics
++ 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 :470
[1] 45908
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/__tmp_chauf_FeFJxDdgsc6*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean gray_scale'
++ Writing one 276x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.sag.png'
++ Writing one 231x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.cor.png'
++ Writing one 231x276 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.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 gray_scale -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 3.29 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 37 45 38 -com SAVE_PNG sagittalimage ./__tmp_ZXCV_img.sag blowup=1 -com SAVE_PNG coronalimage ./__tmp_ZXCV_img.cor blowup=1 -com SAVE_PNG axialimage ./__tmp_ZXCV_img.axi blowup=1 -com QUITT ./__tmp_chauf_FeFJxDdgsc6
\n+* Removing temporary image directory './__tmp_chauf_FeFJxDdgsc6'.\n
++ DONE (good exit)
see: ./__tmp_ZXCV_img*
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
*+ No ylabels entered
*+ No input x-axis; making values based on length of data: [0..449]
++ Will scale each time series by censor_hline
++ Apply scale: 3.3333333333333335
++ Apply scale: 20.0
++ Will apply same y-axis range '[0.0, 3.0]' to all dsets
++ Plotting:
++ Plotting:
++ Done! Figure created:
__tmp_img_enorm.jpg
\n+* Removing temporary files '__tmp_gluing*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_06_mot_grayplot.jpg
rm: No match.
ERROR: QC_FT.NL/media/qc_06_mot_grayplot.pbar.txt not found!!
++ FOR: sum_ideal.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: regressor sum
++ Done! Figure created:
QC_FT.NL/media/qc_07_regr_ideal.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: X.stim.xmat.1D: 2 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: aud#0
++ Plotting: vis#0
++ Done! Figure created:
QC_FT.NL/media/qc_08_regr_stims.jpg
++ Check summary of degrees of freedom in: QC_FT.NL/media/qc_09_regr_df.dat
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay corr_brain+tlrc.HEAD -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_10_regr_corr_errts.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_FT.NL/media/qc_10_regr_corr_errts -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: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: corr_brain+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
++ 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, 1059.000000]
++ 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_BLZD0SdnOo7/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_BLZD0SdnOo7/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[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_s51H8xERyU7XnMhwQSAAPQ 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 = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_s51H8xERyU7XnMhwQSAAPQ+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :948
[1] 46169
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0: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 1059.000000 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -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 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_10_regr_corr_errts.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_10_regr_corr_errts.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_10_regr_corr_errts.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7'.\n
[1] Done Xvfb :948 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_10_regr_corr_errts*
ERROR: QC_FT.NL/media/qc_10_regr_corr_errts.pbar.txt not found!!
++ Prepare for running adjunct_apqc_tsnr_general (ver = 1.1)
++ MODE: 10
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay TSNR.FT.NL+tlrc.HEAD -ulay_range 0% 120% -func_range 322 -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -set_subbricks 0 0 0 -pbar_posonly -blowup 2 -cbar 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -cbar_ncolors 8 -cbar_topval EMPTY -opacity 4 -olay_alpha No -olay_boxed No -thr_olay 0 -pbar_saveim QC_FT.NL/media/qc_11_regr_tsnr_fin.pbar -pbar_comm_range 95%ile in mask -pbar_comm_gen cbar: hot color range (5-95%ile TSNR in mask): 84 - 322 -prefix QC_FT.NL/media/qc_11_regr_tsnr_fin -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: TSNR.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
++ 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, 1059.000000]
++ 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_ac7ziXX1U2B/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_ac7ziXX1U2B/tmp_olay.nii
++ User-entered function range value value (322)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[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_N0u5gfOjMnNaKFqHj1TT0Q 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 = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_N0u5gfOjMnNaKFqHj1TT0Q+tlrc.BRIK
++ 8530021 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 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :638
[1] 46712
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.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=4 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 322 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_11_regr_tsnr_fin.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B'.\n
[1] Done Xvfb :638 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_11_regr_tsnr_fin*
| 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 |
