Hi Paul,
Thank you for answering. As the script worked for the AFNI subject FT I did not check the installation. I apologize for that. The Flask and Flask_cors module were missing and they do seem to be needed for the interactivity of html reports. I rerun "apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json" and it still hangs at qc_02_vorig_olap.
Here is the result of afni_system_check after I installed flask.
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 6.5.0-41-generic
version: #41~22.04.2-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 3 11:32:55 UTC 2
/home/jonathan/abin/afnipy/lib_system_check.py:2126: DeprecationWarning: distro.linux_distribution() is deprecated. It should only be used as a compatibility shim with Python's platform.linux_distribution(). Please use distro.id(), distro.version() and distro.name() instead.
dtest = distro.linux_distribution(full_distribution_name=False)
distribution: ubuntu 22.04 Jammy Jellyfish
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/jonathan/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Apr 18 2024
: AFNI_24.1.03 'Publius Septimius Geta'
AFNI_version.txt : AFNI_24.1.03, linux_ubuntu_16_64, Apr 18 2024, official
which python : /usr/bin/python
python version : 3.8.6
which R : /usr/bin/R
R version : R version 4.1.2 (x86_64-pc-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/jonathan/abin/afni)
R : 1 (/usr/bin/R)
python : 2
/usr/local/bin/python3.8
/home/jonathan/qsmxt_6.4.0_20240209/python
python2 : 0
python3 : 2
/usr/bin/python3.10
/home/jonathan/qsmxt_6.4.0_20240209/python3
** 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 : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /home/jonathan/.local/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.5
++ module loaded: flask
module file : /home/jonathan/.local/lib/python3.8/site-packages/flask/__init__.py
/home/jonathan/abin/afnipy/module_test_lib.py:355: DeprecationWarning: The '__version__' attribute is deprecated and will be removed in Flask 3.1. Use feature detection or 'importlib.metadata.version("flask")' instead.
if hasattr(mod, vfield):
/home/jonathan/abin/afnipy/module_test_lib.py:356: DeprecationWarning: The '__version__' attribute is deprecated and will be removed in Flask 3.1. Use feature detection or 'importlib.metadata.version("flask")' instead.
return getattr(mod, vfield)
flask version : 3.0.3
++ module loaded: flask_cors
module file : /home/jonathan/.local/lib/python3.8/site-packages/flask_cors/__init__.py
flask_cors version : 4.0.1
-- python binaries under /usr/local/bin:
/usr/local/bin/python3.8
/usr/local/bin/python3.6
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/share/fsl/bin:/usr/local/fsl/share/fsl/bin:/home/jonathan/neurodesktop-storage:/usr/local/go/bin:/usr/local/cuda/bin:/home/jonathan/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/jonathan/abin:/home/jonathan/abin:/home/jonathan/qsmxt_6.4.0_20240209:/home/jonathan/abin
PYTHONPATH =
R_LIBS = /home/jonathan/R
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 : found AFNI_data6 under $HOME (350187M Avail)
top history: ... 2024 [rickr]: 3drefit -newid FT/SUMA/FT_SurfVol.nii
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/jonathan/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.11 (amd64)
have Ubuntu system: ubuntu 22.04 Jammy Jellyfish
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Apr 18 2024
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* dot file test : want 1 modifications across 3 files:
The only difference before I installed the module was instead of loading flask it was standing:
"Failed to load module flask".
< -- flask is not required, but is desirable
<
< ** failed to load module flask_cors
< -- flask_cors is not required, but is desirable
After that I run @djunct_overlap_check as you suggested.
@djunct_overlap_check \
-echo \
-ulay mysub/mysub_anat+orig \
-olay mysub/mysub_epi+orig \
-box_focus_slices AMASK_FOCUS_ULAY \
-opacity 4 \
-no_cor \
-no_axi \
-montx_cat 1 \
-monty_cat 1 \
-montx 7 \
-prefix image_test
set more_echo = -echo
else if ( -echo == -prefix ) then
@ ac += 1
end
while ( 2 < = 19 )
if ( ( -ulay == -h ) || ( -ulay == -help ) ) then
if ( -ulay == -ver ) then
if ( -ulay == -ulay ) then
if ( 2 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set ulay = mysub/mysub_anat+orig
else if ( mysub/mysub_anat+orig == -olay ) then
@ ac += 1
end
while ( 4 < = 19 )
if ( ( -olay == -h ) || ( -olay == -help ) ) then
if ( -olay == -ver ) then
if ( -olay == -ulay ) then
if ( -olay == -olay ) then
if ( 4 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set olay = mysub/mysub_epi+orig
else if ( mysub/mysub_epi+orig == -echo ) then
@ ac += 1
end
while ( 6 < = 19 )
if ( ( -box_focus_slices == -h ) || ( -box_focus_slices == -help ) ) then
if ( -box_focus_slices == -ver ) then
if ( -box_focus_slices == -ulay ) then
if ( -box_focus_slices == -olay ) then
if ( -box_focus_slices == -echo ) then
if ( -box_focus_slices == -prefix ) then
if ( -box_focus_slices == -box_focus_slices ) then
if ( 6 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set refbox_add[1] = -box_focus_slices
set refbox_add[2] = AMASK_FOCUS_ULAY
set DO_USE_REFBOX = 1
else if ( AMASK_FOCUS_ULAY == -montgap ) then
@ ac += 1
end
while ( 8 < = 19 )
if ( ( -opacity == -h ) || ( -opacity == -help ) ) then
if ( -opacity == -ver ) then
if ( -opacity == -ulay ) then
if ( -opacity == -olay ) then
if ( -opacity == -echo ) then
if ( -opacity == -prefix ) then
if ( -opacity == -box_focus_slices ) then
if ( -opacity == -montgap ) then
if ( -opacity == -montcolor ) then
if ( -opacity == -ulay_range ) then
if ( -opacity == -ulay_range_nz ) then
if ( -opacity == -cbar ) then
if ( -opacity == -zerocolor ) then
if ( -opacity == -pbar_posonly_off ) then
if ( -opacity == -montx ) then
if ( -opacity == -monty ) then
if ( -opacity == -opacity ) then
if ( 8 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set opacity = 4
else if ( 4 == -label_mode ) then
@ ac += 1
end
while ( 10 < = 19 )
if ( ( -no_cor == -h ) || ( -no_cor == -help ) ) then
if ( -no_cor == -ver ) then
if ( -no_cor == -ulay ) then
if ( -no_cor == -olay ) then
if ( -no_cor == -echo ) then
if ( -no_cor == -prefix ) then
if ( -no_cor == -box_focus_slices ) then
if ( -no_cor == -montgap ) then
if ( -no_cor == -montcolor ) then
if ( -no_cor == -ulay_range ) then
if ( -no_cor == -ulay_range_nz ) then
if ( -no_cor == -cbar ) then
if ( -no_cor == -zerocolor ) then
if ( -no_cor == -pbar_posonly_off ) then
if ( -no_cor == -montx ) then
if ( -no_cor == -monty ) then
if ( -no_cor == -opacity ) then
if ( -no_cor == -label_mode ) then
if ( -no_cor == -edgy_ulay ) then
if ( -no_cor == -set_dicom_xyz ) then
if ( -no_cor == -set_dicom_xyz_off ) then
if ( -no_cor == -montx_cat ) then
if ( -no_cor == -monty_cat ) then
if ( -no_cor == -no_cor ) then
set no_cor = -no_cor
else if ( -no_cor == -no_axi ) then
@ ac += 1
end
while ( 11 < = 19 )
if ( ( -no_axi == -h ) || ( -no_axi == -help ) ) then
if ( -no_axi == -ver ) then
if ( -no_axi == -ulay ) then
if ( -no_axi == -olay ) then
if ( -no_axi == -echo ) then
if ( -no_axi == -prefix ) then
if ( -no_axi == -box_focus_slices ) then
if ( -no_axi == -montgap ) then
if ( -no_axi == -montcolor ) then
if ( -no_axi == -ulay_range ) then
if ( -no_axi == -ulay_range_nz ) then
if ( -no_axi == -cbar ) then
if ( -no_axi == -zerocolor ) then
if ( -no_axi == -pbar_posonly_off ) then
if ( -no_axi == -montx ) then
if ( -no_axi == -monty ) then
if ( -no_axi == -opacity ) then
if ( -no_axi == -label_mode ) then
if ( -no_axi == -edgy_ulay ) then
if ( -no_axi == -set_dicom_xyz ) then
if ( -no_axi == -set_dicom_xyz_off ) then
if ( -no_axi == -montx_cat ) then
if ( -no_axi == -monty_cat ) then
if ( -no_axi == -no_cor ) then
if ( -no_axi == -no_axi ) then
set no_axi = -no_axi
else if ( -no_axi == -no_sag ) then
@ ac += 1
end
while ( 12 < = 19 )
if ( ( -montx_cat == -h ) || ( -montx_cat == -help ) ) then
if ( -montx_cat == -ver ) then
if ( -montx_cat == -ulay ) then
if ( -montx_cat == -olay ) then
if ( -montx_cat == -echo ) then
if ( -montx_cat == -prefix ) then
if ( -montx_cat == -box_focus_slices ) then
if ( -montx_cat == -montgap ) then
if ( -montx_cat == -montcolor ) then
if ( -montx_cat == -ulay_range ) then
if ( -montx_cat == -ulay_range_nz ) then
if ( -montx_cat == -cbar ) then
if ( -montx_cat == -zerocolor ) then
if ( -montx_cat == -pbar_posonly_off ) then
if ( -montx_cat == -montx ) then
if ( -montx_cat == -monty ) then
if ( -montx_cat == -opacity ) then
if ( -montx_cat == -label_mode ) then
if ( -montx_cat == -edgy_ulay ) then
if ( -montx_cat == -set_dicom_xyz ) then
if ( -montx_cat == -set_dicom_xyz_off ) then
if ( -montx_cat == -montx_cat ) then
if ( 12 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set Nx_cat = 1
else if ( 1 == -monty_cat ) then
@ ac += 1
end
while ( 14 < = 19 )
if ( ( -monty_cat == -h ) || ( -monty_cat == -help ) ) then
if ( -monty_cat == -ver ) then
if ( -monty_cat == -ulay ) then
if ( -monty_cat == -olay ) then
if ( -monty_cat == -echo ) then
if ( -monty_cat == -prefix ) then
if ( -monty_cat == -box_focus_slices ) then
if ( -monty_cat == -montgap ) then
if ( -monty_cat == -montcolor ) then
if ( -monty_cat == -ulay_range ) then
if ( -monty_cat == -ulay_range_nz ) then
if ( -monty_cat == -cbar ) then
if ( -monty_cat == -zerocolor ) then
if ( -monty_cat == -pbar_posonly_off ) then
if ( -monty_cat == -montx ) then
if ( -monty_cat == -monty ) then
if ( -monty_cat == -opacity ) then
if ( -monty_cat == -label_mode ) then
if ( -monty_cat == -edgy_ulay ) then
if ( -monty_cat == -set_dicom_xyz ) then
if ( -monty_cat == -set_dicom_xyz_off ) then
if ( -monty_cat == -montx_cat ) then
if ( -monty_cat == -monty_cat ) then
if ( 14 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set Ny_cat = 1
else if ( 1 == -no_cor ) then
@ ac += 1
end
while ( 16 < = 19 )
if ( ( -montx == -h ) || ( -montx == -help ) ) then
if ( -montx == -ver ) then
if ( -montx == -ulay ) then
if ( -montx == -olay ) then
if ( -montx == -echo ) then
if ( -montx == -prefix ) then
if ( -montx == -box_focus_slices ) then
if ( -montx == -montgap ) then
if ( -montx == -montcolor ) then
if ( -montx == -ulay_range ) then
if ( -montx == -ulay_range_nz ) then
if ( -montx == -cbar ) then
if ( -montx == -zerocolor ) then
if ( -montx == -pbar_posonly_off ) then
if ( -montx == -montx ) then
if ( 16 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set Nx = 7
else if ( 7 == -monty ) then
@ ac += 1
end
while ( 18 < = 19 )
if ( ( -prefix == -h ) || ( -prefix == -help ) ) then
if ( -prefix == -ver ) then
if ( -prefix == -ulay ) then
if ( -prefix == -olay ) then
if ( -prefix == -echo ) then
if ( -prefix == -prefix ) then
if ( 18 > = 19 ) goto FAIL_MISSING_ARG
@ ac += 1
set opref = `basename "$argv[$ac]"`
basename image_test
set odir = `dirname "$argv[$ac]"`
dirname image_test
else if ( image_test == -box_focus_slices ) then
@ ac += 1
end
while ( 20 < = 19 )
echo ++ Prepare for running @djunct_overlap_check (ver = 0.46)
++ Prepare for running @djunct_overlap_check (ver = 0.46)
if ( mysub/mysub_anat+orig == ) then
if ( mysub/mysub_epi+orig == ) then
if ( 1 ) then
set user_coors = -pass
endif
mkdir -p .
set wdir = ./__workdir_olap_v5iVdbwyae0
mkdir -p ./__workdir_olap_v5iVdbwyae0
if ( 1 ) then
if ( AMASK_FOCUS_ULAY == AMASK_FOCUS_ULAY || AMASK_FOCUS_ULAY == AMASK_FOCUS_OLAY ) then
echo ++ Using refbox keyword AMASK_FOCUS_ULAY for box_focus_slices
++ Using refbox keyword AMASK_FOCUS_ULAY for box_focus_slices
else
endif
set idx = 0
set uin = mysub/mysub_anat+orig
set uout = olapch_0_cp_ulay.nii
3dcalc -a mysub/mysub_anat+orig -expr a -prefix ./__workdir_olap_v5iVdbwyae0/olapch_0_cp_ulay.nii
++ 3dcalc: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__workdir_olap_v5iVdbwyae0/olapch_0_cp_ulay.nii
@ idx += 1
echo ++ Just copy olay, bc ulay will get regridded
++ Just copy olay, bc ulay will get regridded
set fin = mysub/mysub_epi+orig
set fout = olapch_1_cp_olay.nii
3dcalc -a mysub/mysub_epi+orig -expr a -prefix ./__workdir_olap_v5iVdbwyae0/olapch_1_cp_olay.nii
++ 3dcalc: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__workdir_olap_v5iVdbwyae0/olapch_1_cp_olay.nii
@ idx += 1
cd ./__workdir_olap_v5iVdbwyae0
set newsp = `3dinfo -space "${fout}"`
3dinfo -space olapch_1_cp_olay.nii
echo ++ Quietly run: 3drefit -space ORIG olapch_0_cp_ulay.nii
++ Quietly run: 3drefit -space ORIG olapch_0_cp_ulay.nii
3drefit -space ORIG olapch_0_cp_ulay.nii
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -box_focus_slices AMASK_FOCUS_ULAY -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 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -no_cor -no_axi -pass -pass
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -box_focus_slices AMASK_FOCUS_ULAY -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 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -no_cor -no_axi -pass -pass
++ Using AFNI ver : AFNI_24.1.03
++ chauffeur ver : 6.7
------------------ start of optionizing ------------------
++ 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_EBL5gTkvuvb
++ 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, 576.000000]
++ 3dcalc: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_EBL5gTkvuvb/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_EBL5gTkvuvb/tmp_olay.nii
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /home/jonathan/projects/thdc/Principal_Investigator/MR0000_Test/__workdir_olap_v5iVdbwyae0/__tmp_chauf_EBL5gTkvuvb/tmp_olay.nii,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/home/jonathan/projects/thdc/Principal_Investigator/MR0000_Test/__workdir_olap_v5iVdbwyae0/__tmp_chauf_EBL5gTkvuvb/tmp_olay.nii is 13.409355 degrees from plumb.
++ For olay, the 98%ile value leads to
--> upper range value: 1528.000000
++ Dimensions (xyzt): 240 256 208 1
++ (initial) Slice spacing ordered (x,y,z) is: 29 34 36
++ 3dAutomask: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Authored by: Emperor Zhark
++ 3dAutobox: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Auto bbox: x=1..231 y=25..255 z=20..189
++ 3dAutobox: output dataset = ./__tmp_chauf_EBL5gTkvuvb/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_EBL5gTkvuvb/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_P8RA3EPlJo_CCqsf-Rs1TQ argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_24.1.03 (Apr 18 2024) [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
++ 9071370 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ -4 -29 -21
++ Will have the ref box central gapord: 24 33 33
------------------- end of optionizing -------------------
-- trying to start Xvfb :554
[1] 581991
+++ 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=7x1:24:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=7x1:33:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=7x1:33:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 576.000000 -com SET_FUNC_RANGE 1528.000000 -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_DICOM_XYZ -4 -29 -21 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com QUITT ./__tmp_chauf_EBL5gTkvuvb
+/home/jonathan/projects/thdc/Principal_Investigator/MR0000_Test/__workdir_olap_v5iVdbwyae0/__tmp_chauf_EBL5gTkvuvb
Jonathan
