Dear developers,
I get an error in the QC step** (output.proc)
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
++ Done making (executable) IC pbrun script:
run_instacorr_pbrun.tcsh
++ Done making (executable) GV pbrun script:
run_graphview_pbrun.tcsh
++ 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
++ APQC create: qc_05_mot_enormoutlr
++ APQC create: qc_06_mot_VR6
++ APQC create: qc_07_mecho_mtedana
++ APQC create: qc_08_regr_df
++ APQC create: qc_09_regr_tsnr_fin
Traceback (most recent call last):
File "/home/taliw/abin/apqc_make_tcsh.py", line 912, in <module>
cmd = lat.apqc_regr_tsnr( ap_ssdict, obase, "regr", "tsnr_fin",
File "/home/taliw/abin/afnipy/lib_apqc_tcsh.py", line 3760, in apqc_regr_tsnr
lll = com.so[0].split()
IndexError: list index out of range
AFNI version info (afni -ver):
Precompiled binary linux_ubuntu_16_64: Sep 29 2023 (Version AFNI_23.2.12 'Marcus Didius Severus Julianus')
>>afni_system_check.py -check_all
> -------------------------------- general ---------------------------------
> architecture: 64bit ELF
> cpu type: x86_64
> system: Linux
> release: 5.13.0-39-generic
> version: #44~20.04.1-Ubuntu SMP Thu Mar 24 16:43:35 UTC 2022
> distribution: ubuntu 20.04 focal
> number of CPUs: 16
> apparent login shell: bash
> shell RC file: .bashrc (exists)
>
> --------------------- AFNI and related program tests ---------------------
> which afni : /home/taliw/abin/afni
> afni version : Precompiled binary linux_ubuntu_16_64: Sep 29 2023
> : AFNI_23.2.12 'Marcus Didius Severus Julianus'
> AFNI_version.txt : AFNI_23.2.12, linux_ubuntu_16_64, Sep 29 2023, official
> which python : /usr/bin/python
> python version : 3.8.10
> which R : /usr/bin/R
> R version : R version 3.6.3 (x86_64-pc-linux-gnu)
>
> instances of various programs found in PATH:
> afni : 1 (/home/taliw/abin/afni)
> R : 1 (/usr/bin/R)
> python : 1 (/usr/bin/python3.8)
> python2 : 1 (/usr/bin/python2.7)
> python3 : 1 (/usr/bin/python3.8)
>
>
> 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/taliw/.local/lib/python3.8/site-packages/matplotlib/pyplot.py
> matplotlib version : 3.4.3
>
> -------------------------------- env vars --------------------------------
> PATH = :/opt/ANTs/bin/:/opt/anaconda3/condabin:/opt/mrtrix3/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/fsl/bin:/opt/freesurfer/mni/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/opt/fsl/bin:/home/taliw/.local/bin:/home/taliw/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/taliw/.local/bin:/home/taliw/workbench/bin_linux64:/home/taliw/abin
>
> PYTHONPATH =
> R_LIBS = /home/taliw/R
>
> LD_LIBRARY_PATH =
> DYLD_LIBRARY_PATH =
> DYLD_FALLBACK_LIBRARY_PATH =
>
> ----------------------------- 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, flatdir, apsearch
> (not on a mac, should skip flatdir)
>
> -- note: followers should not need edits, so edit flags should be 0
> (have 1 follower(s), which can be ignored)
>
> no modifications needed across 3 dot files
>
> ------------------------------ 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 /home/taliw/abin
>
> ------------------------------ OS specific -------------------------------
> which apt-get : /usr/bin/apt-get
> apt-get version : apt 2.0.9 (amd64)
>
> have Ubuntu system: ubuntu 20.04 focal
> have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Sep 29 2023
>
> ========================= summary, please fix: =========================
> * just be aware: login shell 'bash', but our code examples use 'tcsh'
> * insufficient data for AFNI bootcamp
> (see "Prepare for Bootcamp" on install pages)