APQC output issues

mjss · June 7, 2021, 9:35pm

Dear AFNI experts,

I am attempting to follow the AFNI bootcamp tutorial but am encountering some errors when analyzing the FT data from AFNI_data6. I am able to run the sample s05.ap.uber script, and the resulting proc.FT script. However, this latter script returns some errors towards the end of the script during the APQC stage. Some of the QC files are missing (e.g., no .html file) and the @ss_review driver scripts return errors. I get the same errors when attempting to run the basic or pythonic html_review_style. I have python and matplotlib installed. The out.proc file shows some errors early in the apqc_make_tcsh.py script, such as ERROR: QC_FT/media/qc_00_vorig_EPI.pbar.txt not found!! but I am not sure how to interpret this. I have attached a screenshot of the output.proc.FT log file starting at the apqc_make_tcsh.py section in the hopes that someone can help shed some light on the issue.

Many thanks,

Michael

ptaylor · June 7, 2021, 9:56pm

Hi, Michael-

OK—could you please copy+paste the output of this command, so we can first doublecheck the setup on that machine:


afni_system_check.py -check_all

?

thanks,
pt

mjss · June 8, 2021, 12:49am

Thank you. Please see below for the output.
Michael

[Michaels-MacBook-Pro-6:~] michaelspilka% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
distribution: 10.14.5
number of CPUs: 4
apparent login shell: bash (current shell is csh)
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/michaelspilka/abin/afni
afni version : Precompiled binary macos_10.12_local: Apr 16 2021
: AFNI_21.1.02 ‘Domitian’
AFNI_version.txt : AFNI_21.1.02, macos_10.12_local, Apr 16 2021
which python : /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python
python version : 3.8.8
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) – “Holding the Windsock”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/michaelspilka/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
/Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python3.8
/usr/bin/python
python2 : 0
python3 : 2
/Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python3.8
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6

** have python3 but not python2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

R RHOME : /Library/Frameworks/R.framework/Resources

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/lib/python3.8/site-packages/matplotlib/pyplot.py

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

-------------------------------- env vars --------------------------------
PATH = /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin:/Users/michaelspilka/miniconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/workbench/bin_macosx64:/Users/michaelspilka/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/michaelspilka/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.0_beta4

which brew : /usr/local/bin/brew
brew version : Homebrew 3.1.7

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
** consider linking /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.68.1/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘csh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
insufficient data for AFNI bootcamp

ptaylor · June 8, 2021, 1:53am

Thanks for sending that system check output. I don’t think anything there looks weird to me.

Soooo… I’m not sure why that failed. I just reran the s05* script from the Bootcamp on a Mac, using the current binaries, and it worked fine.

Perhaps, could you try updating your binaries:


@update.afni.binaries -d

… and see if that solves the issue?

After updating your binaries, if you don’t want to run the whole afni_proc.py script again, you could get navigate to your afni_proc.py output “results” directory, and run the followign to download a script to re-run just the QC there:


curl -O https://raw.githubusercontent.com/afni/afni/master/src/ptaylor/supplement/redo_apqc.tcsh

… and then run this:


tcsh redo_apqc.tcsh

It will push any current QC_[subject] directory to old_QC_[subject]_[timestamp], and the re-run the QC again. Please let me know how that goes.

–pt

mjss · June 8, 2021, 2:10pm

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*

mjss · June 8, 2021, 2:11pm

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
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%

mjss · June 8, 2021, 10:01pm

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

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

[Michaels-MacBook-Pro-6:AfniBootcamp/AFNI_data6/FT_analysis] michaelspilka% tcsh s00.warper_MS
++ Starting: @SSwarper v2.5
++ Default OMP_NUM_THREADS is 4
++ Prepare for running @djunct_overlap_check (ver = 0.3)
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./FT/anat_warped/__workdir_olap_On0GkWOz9Vf/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./FT/anat_warped/__workdir_olap_On0GkWOz9Vf/olapch_1_cp_olay.nii
++ 3drefit: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset olapch_0_cp_ulay.nii
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also

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

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

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

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

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

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

++ DONE! Image output:
FT/anat_warped/init_qc_00_overlap_usrc_obase

ptaylor · June 9, 2021, 9:02pm

Hi-

Thanks for posting those.

Unfortunately, I am stumped. I have re-run the QC html generation and @SSwarper using the latest code on both my Linux (Ubuntu 20.04) and on my Mac (10.15). On Linux, I used both Python 3.7 and 3.8—everything worked fine in all cases. On Mac, I used Python 3.7 and 3.8 as well. I don’t get those error messages.

Taking a step back: @chauffeur_afni is a script that takes command line options to build a command to the afni GUI to load up data and view it in a certain way (colorbar, location, montage, etc.) and then save an image or movie from it. I can see in the output text that there are some odd things happening in the driven ‘afni’ GUI command. The issue I have is that I don’t see how the also displayed @chauffeur_afni command creates that badness—it looks fine, and when I run the sames types of commands on my systems, the command behaves as it should.

It looks like you only have 1 version of AFNI on your system, and your path looks pretty straightforward, so that should mean there shouldn’t be any mixing of different AFNI versions happening. Also, it looks like most of the instances of this are actually working, it is just one or two that are failing. Ummmm, this is perplexing.

As another test, could you please run each of the following; and if you are using tcsh terminal shell, could you please add the funny looking “|& tee -a log_testingC.txt”, but if you use a bash or zsh shell, could you please add the serious looking “2>&1 | tee -a log_testingB.txt”:


@chauffeur_afni                                   \
    -ulay FT_anat+orig.HEAD                       \
    -olay FT_anat+orig.HEAD                       \
    -ulay_range_nz 0 1300                         \
    -func_range    1300                           \
    -box_focus_slices AMASK_FOCUS_ULAY            \
    -cbar gray_scale                              \
    -pbar_posonly                                 \
    -pbar_saveim TEST1.pbar.jpg                   \
    -pbar_comm_range "test1 text"                  \
    -pbar_for dset                                \
    -prefix      TEST1                            \
    -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

@chauffeur_afni                                   \
    -ulay FT_anat+orig.HEAD                       \
    -olay FT_anat+orig.HEAD                       \
    -ulay_range_nz 0 1300                         \
    -func_range    1300                           \
    -box_focus_slices AMASK_FOCUS_ULAY            \
    -cbar gray_scale                              \
    -pbar_posonly                                 \
    -pbar_comm_range "test2 text"                 \
    -pbar_for dset                                \
    -prefix      TEST2                            \
    -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

…

And could you please let me know 1) which files are output, and 2) what the log*txt file contains?

thanks,
pt

mjss · June 10, 2021, 3:49pm

Thanks so much for your continued help with this. For each script, 3 image files are output (axial, coronal, sagittal) of a 3x3 slice montage without colorbars. The log files look nearly identical for both. I have copied the content for each below. One thing I noticed when looking at my afni_system_check is that although I am running Python 3.8 set up through Miniconda, it looks like the Python binaries are listed as Python 3.6. Would this be an issue? (see below)
python3 : 2
/Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python3.8
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6

++ module loaded: matplotlib.pyplot
module file : /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/lib/python3.8/site-packages/matplotlib/pyplot.py

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

Output for @chauffeur_afni scripts:
1:
++ My command:
@chauffeur_afni -ulay FT_anat+orig.HEAD -olay FT_anat+orig.HEAD -ulay_range_nz 0 1300 -func_range 1300 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim TEST1.pbar.jpg -pbar_comm_range test1 text -pbar_for dset -prefix TEST1 -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: FT_anat+orig.HEAD
++ Found input file: FT_anat+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_X1vYw23kNow
++ 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, 1367.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_X1vYw23kNow/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_X1vYw23kNow/tmp_olay.nii
++ User-entered function range value value (1300)
++ Dimensions (xyzt): 256 256 175 1
++ (initial) Slice spacing ordered (x,y,z) is: 19 28 28
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=FT_anat+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__NIEBKAc_v6IeDbIB2yG8g argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.062029
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN__NIEBKAc_v6IeDbIB2yG8g+orig.BRIK
++ 11468800 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 128 127 86
\n------------------- end of optionizing -------------------\n
– trying to start Xvfb :12
[1] 84203
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT/__tmp_chauf_X1vYw23kNowe[7m*+ WARNING:e[0m Bad drive AFNI result from ‘SET_PBAR_ALL +99 -do_clean gray_scale’
++ Writing one 3072x3072 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > ./TEST1.sag.png’
++ Writing one 2240x3072 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > ./TEST1.cor.png’
++ Writing one 2240x3072 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > ./TEST1.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=3x3:19:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:28:0: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 1367.000000 -com SET_FUNC_RANGE 1300 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 128 127 86 -com SAVE_PNG sagittalimage ./TEST1.sag blowup=4 -com SAVE_PNG coronalimage ./TEST1.cor blowup=4 -com SAVE_PNG axialimage ./TEST1.axi blowup=4 -com QUITT ./__tmp_chauf_X1vYw23kNow

\n+* Removing temporary image directory ‘./__tmp_chauf_X1vYw23kNow’.\n

++ DONE (good exit)
see: ./TEST1*

2:
++ My command:
@chauffeur_afni -ulay FT_anat+orig.HEAD -olay FT_anat+orig.HEAD -ulay_range_nz 0 1300 -func_range 1300 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_comm_range test2 text -pbar_for dset -prefix TEST2 -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: FT_anat+orig.HEAD
++ Found input file: FT_anat+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_wQMY7brYUQG
++ 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, 1367.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_wQMY7brYUQG/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_wQMY7brYUQG/tmp_olay.nii
++ User-entered function range value value (1300)
++ Dimensions (xyzt): 256 256 175 1
++ (initial) Slice spacing ordered (x,y,z) is: 19 28 28
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=FT_anat+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_PLAZKjh37xw2Cm9b8xKCLg argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.062029
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_PLAZKjh37xw2Cm9b8xKCLg+orig.BRIK
++ 11468800 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 128 127 86
\n------------------- end of optionizing -------------------\n
– trying to start Xvfb :157
[1] 84387
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT/__tmp_chauf_wQMY7brYUQGe[7m*+ WARNING:e[0m Bad drive AFNI result from ‘SET_PBAR_ALL +99 -do_clean gray_scale’
++ Writing one 3072x3072 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > ./TEST2.sag.png’
++ Writing one 2240x3072 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > ./TEST2.cor.png’
++ Writing one 2240x3072 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > ./TEST2.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=3x3:19:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:28:0: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 1367.000000 -com SET_FUNC_RANGE 1300 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_IJK 128 127 86 -com SAVE_PNG sagittalimage ./TEST2.sag blowup=4 -com SAVE_PNG coronalimage ./TEST2.cor blowup=4 -com SAVE_PNG axialimage ./TEST2.axi blowup=4 -com QUITT ./__tmp_chauf_wQMY7brYUQG

\n+* Removing temporary image directory ‘./__tmp_chauf_wQMY7brYUQG’.\n

++ DONE (good exit)
see: ./TEST2*

ptaylor · June 10, 2021, 10:23pm

Thanks for sending that.

I don’t think this is a Python issue.

Something is funny with how the options are being read in. The reason that the “Bad drive” occurs is because “-do_clean” gets inserted where it shouldn’t, and the option to insert a value at that location is not used.

Additionally, comparing your terminal output to mine, I see that even this information is not being interpreted correctly: “-ulay_range_nz 0 1300”. Basically, that should lead to this line in the output:


++ Ulay to be visualized within user range:
   [0, 1300]

… because the ulay range is being explicitly stated. However, in yours, it looks like this:


++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1367.000000]

… which is the default behavior if the utilized option were not being used.

So, this is mysterious. And somehow a shell issue, I think.

I made an update to @chauffeur_afni that will allow some more verbose output. Could you please go to the same Bootcamp dir, AFNI_data6/FT_analysis/FT, and copy+paste the following:


curl -O [https://raw.githubusercontent.com/afni/afni/f72a8d64acba0a26eb4292bdb326bf300bae2615/src/scripts_install/%40chauffeur_afni](https://raw.githubusercontent.com/afni/afni/f72a8d64acba0a26eb4292bdb326bf300bae2615/src/scripts_install/%40chauffeur_afni)

Then, can you run these slightly modified chauffeur commands (each now contains “-echo” as the first option, and also they are executed with “tcsh ./@chauffeur_afni …” to specify that this specific version of the program should be used), and save the output of each to a log in the same way as before (redirecting, appropriate to what shell you are running)?:


tcsh ./@chauffeur_afni  -echo                                 \
    -ulay FT_anat+orig.HEAD                       \
    -olay FT_anat+orig.HEAD                       \
    -ulay_range_nz 0 1300                         \
    -func_range    1300                           \
    -box_focus_slices AMASK_FOCUS_ULAY            \
    -cbar gray_scale                              \
    -pbar_posonly                                 \
    -pbar_saveim TEST1.pbar.jpg                   \
    -pbar_comm_range "test1 text"                  \
    -pbar_for dset                                \
    -prefix      TEST1                            \
    -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

tcsh ./@chauffeur_afni -echo                                  \
    -ulay FT_anat+orig.HEAD                       \
    -olay FT_anat+orig.HEAD                       \
    -ulay_range_nz 0 1300                         \
    -func_range    1300                           \
    -box_focus_slices AMASK_FOCUS_ULAY            \
    -cbar gray_scale                              \
    -pbar_posonly                                 \
    -pbar_comm_range "test2 text"                 \
    -pbar_for dset                                \
    -prefix      TEST2                            \
    -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

These outputs will be verbose. Could you please email me the text files of them (I will email you so you have my email).

Thanks,
pt