Hello,
The "NV" button in QC HTML isn't responding after clicking (processed in Rocky Linux). I have flask and flask_cors installed. This also happens when running the same code in WSL (Ubuntu). Do I need to specify some options in afni_proc.py? I do set -html_review_style pythonic
. The "RATE" button appears to be struck through and A, A+ etc are also not responding. Could you please help to fix this?
Here is afni_system_check.py -check_all result
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: AMD EPYC 7532 32-Core Processor
system: Linux
release: 4.18.0-513.24.1.el8_9.x86_64
version: #1 SMP Thu Apr 4 18:13:02 UTC 2024
distribution: Rocky Linux 8.9 (Green Obsidian)
number of CPUs: 64
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin/afni
afni version : Precompiled binary 1: Apr 19 2024
: AFNI_99.99.99 'Alexios V Doukas the Bushy-eyebrowed'
AFNI_version.txt :
which python : /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/python/3.11.5/bin/python
python version : 3.11.5
which R : /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.3.1/bin/R
R version : R version 4.3.1 (x86_64-pc-linux-gnu)
instances of various programs found in PATH:
afni : 2
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin/afni
/home/djangoc/abin/afni
R : 1 (/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.3.1/bin/R)
python : 2
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/python/3.11.5/bin/python3.11
/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/python-exec2c
python2 : 0
python3 : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/python/3.11.5/bin/python3.11
/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/python-exec2c
/usr/libexec/platform-python3.6
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/tcsh
which Xvfb : /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.3.1/lib64/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/scipy-stack/2023b/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.2
++ module loaded: flask
module file : /home/djangoc/.local/lib/python3.11/site-packages/flask/__init__.py
flask version : 3.0.3
++ module loaded: flask_cors
module file : /home/djangoc/.local/lib/python3.11/site-packages/flask_cors/__init__.py
flask_cors version : 4.0.0
-------------------------------- env vars --------------------------------
PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/scipy-stack/2023b/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/ipykernel/2023b/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/python/3.11.5/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/protobuf/24.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/fftw/3.3.10/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/netcdf/4.9.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/hdf5/1.14.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/gsl/2.7/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/qt/5.15.11/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.3.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/java/17.0.6:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/java/17.0.6/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/openmpi/4.1.5/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/ucc/1.2.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/pmix/4.2.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/libfabric/1.18.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/ucx/1.14.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/hwloc/2.9.1/sbin:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/hwloc/2.9.1/bin:/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/x86_64-pc-linux-gnu/gcc-bin/12:/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/mii/1.1.2/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin:/cvmfs/soft.computecanada.ca/custom/bin/computecanada:/home/djangoc/.local/bin:/home/djangoc/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/djangoc/abin
PYTHONPATH = /cvmfs/soft.computecanada.ca/easybuild/python/site-packages:/cvmfs/soft.computecanada.ca/custom/python/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.7.0
which yum : /usr/bin/yum
yum version : 4.7.0
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing AFNI_version.txt, maybe package is old
* failure under initial "AFNI and related program tests"
* have multiple versions of AFNI in PATH
* dot file test : want 1 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* possibly missing atlases
Here is the output chuck related to QC
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
++ Done making (executable) IC errts script:
run_instacorr_errts.tcsh
++ Done making (executable) GV errts script:
run_graphview_errts.tcsh
++ Done making (executable) IC pbrun script:
run_instacorr_pbrun.tcsh
++ Done making (executable) GV pbrun script:
run_graphview_pbrun.tcsh
+* WARNING: cannot find logo file:
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin/apqc_logo_main.svg
+* WARNING: cannot find logo file:
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin/apqc_logo_help.svg
+* WARNING: cannot find font file:
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin/FiraCode-Bold.woff2
+* WARNING: cannot find font file:
/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcc12/afni/24.1.03/bin/FiraCode-Regular.woff2
++ APQC create: qc_00_vorig_EPI
++ APQC create: qc_01_vorig_anat
++ APQC create: qc_02_vorig_olap
++ APQC create: qc_03_ve2a_epi2anat
++ APQC create: qc_04_ve2a_mask2final
++ Found 3 stats items to use for vstat QC block
++ APQC create: qc_05_vstat_Full_Fstat
++ APQC create: qc_06_vstat_type1_0_Coef
++ APQC create: qc_07_vstat_type2_0_Coef
++ APQC create: qc_08_mot_enormoutlr
++ APQC create: qc_09_mot_VR6
++ APQC create: qc_10_mot_grayplot
++ APQC create: qc_11_regr_ideal
++ APQC create: qc_12_regr_stims
++ APQC create: qc_13_regr_df
++ APQC create: qc_14_regr_corr_errts
++ APQC create: qc_15_regr_tsnr_vreg
++ APQC create: qc_16_regr_tsnr_fin
++ APQC create: qc_17_radcor_rc_tcat
run: r01/9
run: r02/9
run: r03/9
run: r04/9
run: r05/9
run: r06/9
run: r07/9
run: r08/9
run: r09/9
++ APQC create: qc_18_radcor_rc_volreg
run: r01/9
run: r02/9
run: r03/9
run: r04/9
run: r05/9
run: r06/9
run: r07/9
run: r08/9
run: r09/9
++ APQC create: qc_19_warns_xmat
++ APQC create: qc_20_warns_cen_total
++ APQC create: qc_21_warns_cen_stim
++ APQC create: qc_22_warns_decon
++ APQC create: qc_23_warns_press
++ APQC create: qc_24_warns_sat_4095
++ APQC create: qc_25_warns_flip
++ APQC create: qc_26_warns_vlines
++ APQC create: qc_27_qsumm_ssrev
++ APQC create: copy jsons to info dir
++ APQC create: copy ss_review_basic file
++ APQC create: display ss_review_basic info