Hi,
I installed afni on a Linux cloud system via conda. While running afni_proc.py on multiple data sets, I keep getting errors about mask.nii.gz:
++ requiring 5 voxels in mask columns
++ 3dLocalstat: AFNI version=AFNI_23.1.08 (Jul 7 2023) [64-bit]
++ Authored by: Emperor Zhark
** AFNI can't deal with 5 dimensional NIfTI(/mnt/work/ADTime/mae/derivatives/sub$
** FATAL ERROR: Can't open dataset 'mask.nii.gz'
** Program compile date = Jul 7 2023
++ 3dcalc: AFNI version=AFNI_23.1.08 (Jul 7 2023) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset tmp.mask.col.count.nii.gz
** Program compile date = Jul 7 2023
This is the AFNI version I'm using (afni -ver) (although same happens with version 23.1.10):
Precompiled binary 1: Jul 7 2023 (Version AFNI_23.1.08 'Publius Helvius Pertinax')
And the output of afni_system_check.py -check_all:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Linux
release: 4.15.0-214-generic
version: #225-Ubuntu SMP Thu Jul 13 09:22:47 UTC 2023
distribution: debian buster/sid
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/maetg/mambaforge/envs/py36/bin/afni
afni version : Precompiled binary 1: Jul 7 2023
: AFNI_23.1.08 'Publius Helvius Pertinax'
AFNI_version.txt :
which python : /home/maetg/mambaforge/envs/py36/bin/python
python version : 3.6.15
which R : /home/maetg/mambaforge/envs/py36/bin/R
R version : R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
instances of various programs found in PATH:
afni : 1 (/home/maetg/mambaforge/envs/py36/bin/afni)
R : 2
/home/maetg/mambaforge/envs/py36/bin/R
/usr/bin/R
python : 2
/home/maetg/mambaforge/envs/py36/bin/python3.6
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/home/maetg/mambaforge/envs/py36/bin/python3.6
/usr/bin/python3.6
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 : /home/maetg/mambaforge/envs/py36/lib/R
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /home/maetg/mambaforge/envs/py36/lib/python3.6/site-packages/matplotlib/pyplot.py
matplotlib version : 3.3.4
-------------------------------- env vars --------------------------------
PATH = /home/maetg/mambaforge/envs/py36/bin:/home/maetg/mambaforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PYTHONPATH =
R_LIBS =
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 ----------
-- no .tcshrc, will create one as a follower of .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)
dot file test : want 3 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 1 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 1 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 /home/maetg/mambaforge/envs/py36/share/AFNI/data
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.17 (amd64)
========================= 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"
* dot file test : want 3 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
Any idea how to resolve this? I have checked the other threads related to this issue but unfortunately haven't found a solution.
Thanks!