Hi Paul.
Thanks for the tips and the links to the poster and demo for ME processing. I've put the results of the system check at the bottom. My responses are below.
Best,
Alex
> So, that RetroTS.py program does have pylab as a module dependency. I would have thought
> installing matplotlib would install that as well, in most situations.
I probably need to put the pylab module inside my virtual Python environment. I'm still figuring out how to configure all of that, and will work with the people who manage our cluster.
> In the scripts_desktop_do_14_physio.tcsh, is this example command:
RetroTS.py -prefix ${subj}_${ses}_${task_label} \
-r ${physio_resp} \
-c ${physio_card} \
-p 50 -n 33 -v 2.2
> ... where "-v 2.2" signifies a volumetric TR of 2.2s, and "-n 33" means that the volume has n=33 slices. The multi-echo aspect comes in when you
> process all the EPI information, combining them into a single value per TR (through, for example,
> optimal combination (OC) or tedana). In the demo, that FMRI processing is done using afni_proc.py
> and there are various ME-combination methods: OC, old Kundu et al. MEICA and newer MEICA group
> tedana (mtedana).
Thanks for the clarification on the structure of the RetroTS.py script. That now makes sense to me.
> Could you perphaps copy+paste the output of:
>
> afni_system_check.py -check_all
>
> on that system?
Here are the results of running afni_system_check.py -check_all
FinalScripts$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 4.4.0-206-generic
version: #238-Ubuntu SMP Tue Mar 16 07:52:37 UTC 2021
distribution: debian stretch/sid
number of CPUs: 24
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/global/afni/23.0.07/afni
afni version : Precompiled binary linux_ubuntu_16_64: Mar 1 2023
: AFNI_23.0.07 'Commodus'
AFNI_version.txt : AFNI_23.0.07, linux_ubuntu_16_64, Mar 01 2023
which python : /remote_home/stevenal/myenvs/py3/bin/python
python version : 3.7.9
which R : /usr/bin/R
R version : R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 3
/usr/global/afni/23.0.07/afni
/usr/lib/afni/bin/afni_wrapper
/usr/lib/afni/bin/afni
R : 1 (/usr/bin/R)
python : 2
/usr/global/python/versions/pypy3.7-7.3.3/bin/pypy3
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/usr/global/python/versions/pypy3.7-7.3.3/bin/pypy3
/usr/bin/python3.5
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 : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
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
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
-------------------------------- env vars --------------------------------
PATH = /usr/global/afni/23.0.07:/remote_home/stevenal/myenvs/py3/bin:/usr/global/freesurfer/7.1.1/bin:/usr/global/freesurfer/7.1.1/fsfast/bin:/usr/global/freesurfer/7.1.1/tktools:/usr/global/fsl/6.0.4/bin:/usr/global/freesurfer/6.0.0/mni/bin:/usr/lib/fsl/5.0:/remote_home/stevenal/bin:/remote_home/stevenal/.local/bin:/remote_home/stevenal/abin:/usr/global/freesurfer/6.0.0/bin:/usr/global/freesurfer/6.0.0/fsfast/bin:/usr/global/freesurfer/6.0.0/tktools:/usr/global/camino/bin:/usr/global/ants/2.1.0-xenial/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/afni/bin:/usr/global/bin:/usr/global/4dfp/bin:/usr/global/btk/Applications:/usr/global/btk/Utilities:/usr/global/btk/Scripts:/usr/global/btk/Viewer:/usr/global/caret/bin_linux64:/usr/global/dtiquery-1.1:/usr/global/dtitk/2.3.1/bin:/usr/global/dtitk/2.3.1/utilities:/usr/global/dtitk/2.3.1/scripts
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/lib/fsl/5.0
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
** warning: .tcshrc does NOT seem to contain 'source .cshrc'
-- (csh and tcsh will use different files)
-- considered opertaions: path, flatdir, apsearch
(not on a mac, should skip flatdir)
-- note: followers should not need edits, so edit flags should be 0
(have 0 follower(s), which can be ignored)
dot file test : want 5 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 1 0 1 0
.tcshrc 1 0 1 0
.bashrc 1 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 : found TT_N27+tlrc under /usr/global/afni/20.3.02
atlas : found TT_N27+tlrc under /usr/share/afni/atlases
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.2.32ubuntu0.2 (amd64)
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* have multiple versions of AFNI in PATH
* missing R packages (see rPkgsInstall)
* python library matplotlib is required
(see AFNI install docs for details)
* dot file test : want 5 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
