Install issues Mac Sonoma 14.6 Intel

Hello,
I am having issues with my AFNI installation on Mac 14.6 with Intel processor and OS Sonoma 14.6.1.
I searched the forum for possible solutions but other cases appear to be slightly different and also I am not familiar with Mac terminal or AFNI installations. If anyone has any suggestions on what I could try I greatly appreciate it.

I am performing the steps as described here
1.1.9. macOS 12+ (Intel processor/chip) — AFNI, SUMA and FATCAT: v25.0.02.

I do not have any errors for the first two steps
B. zsh OS_notes.macos_12_intel_a_admin_pt1.zsh
C. zsh OS_notes.macos_12_intel_a_admin_pt2.zsh

However, after restarting and running the last command
tcsh OS_notes.macos_12_intel_b_user.tcsh
I get several errors.

----ERROR 1-----
++ building (please be patient)...

++ need alternate compiler, trying /usr/local/bin/gcc-14
(if this fails, try passing one via -cc_path)

** error: failed run_cmd: make AFNI_WHOMADEIT=build LOCAL_CC_PATH=/usr/local/bin/gcc-14 itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/laptop1/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:

----ERROR 2-----
mv: rename dcm2niix_afni to macos_12_x86_64/dcm2niix_afni: No such file or directory
make: *** [install] Error 1

Here is the output from the
afni_system_check.py -check_all

-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Mon Jul 29 21:13:00 PDT 2024; root:xnu-10063.141.2~1/RELEASE_X86_64
distribution: 10.16 (sw_vers 14.6.1)
number of CPUs: 8
user: laptop1
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.0.01, anyos_text, Jan 29 2025, local
which python : /Users/laptop1/miniconda3/bin/python
python version : 3.12.8
which R : /usr/local/bin/R
R version : R version 4.3.1 (x86_64-apple-darwin20)

instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/bin/R)
python : 2
/Users/laptop1/miniconda3/bin/python3.12
/usr/local/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
python2 : 0
python3 : 3
/Users/laptop1/miniconda3/bin/python3.12
/usr/local/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/usr/bin/python3

testing ability to start various programs...
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
uber_subject.py : success
3dMVM : FAILURE
Error in library(data.table) : there is no package called ‘data.table’
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
rPkgsInstall : FAILURE

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh : /bin/tcsh
tcsh version : 6.21.00
which Xvfb : /opt/X11/bin/Xvfb

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

R RHOME : /Library/Frameworks/R.framework/Resources

------------------------------ python libs -------------------------------

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required

** 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

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13)

-------------------------------- env vars --------------------------------
PATH = /Users/laptop1/miniconda3/bin:/Users/laptop1/miniconda3/condabin:/usr/local/bin:/usr/local/sbin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/usr/local/opt/python/libexec/bin:/Users/laptop1/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin

PYTHONPATH (sub-shell) =
R_LIBS = /Users/laptop1/sw/R-4.3.1
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
CC (sub-shell) =

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

.afnirc                   : found
.sumarc                   : missing
.afni/help/all_progs.COMP : missing

--------- 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)

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 : found afni_handouts under $HOME/OneDrive/NOS
atlas : did not find TT_N27+tlrc

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5

which brew : /usr/local/bin/brew
brew version : Homebrew 4.4.20

which git : /usr/bin/git
git version : git version 2.39.5 (Apple Git-154)
which gcc : /usr/bin/gcc
gcc version : Apple clang version 16.0.0 (clang-1600.0.26.4)

brew gcc(s) : /usr/local/bin/gcc-14
CommandLineTools SDK : MacOSX15.1.sdk
** consider linking /usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.82.4/lib/libglib-2.0.dylib

========================= summary, please fix: =========================

  • just be aware: login shell 'zsh', but our code examples use 'tcsh'
  • missing program: afni
  • failure under initial "AFNI and related program tests"
  • AFNI programs show FAILURE
  • missing R packages (see rPkgsInstall)
  • python library matplotlib is required
    (see AFNI install docs for details)
  • please run: "suma -update_env" for .sumarc
  • please run: apsearch -update_all_afni_help
  • insufficient data for AFNI bootcamp
    (see "Prepare for Bootcamp" on install pages)
  • possibly missing atlases
  • consider linking /usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib

laptop1@laptop1-MacBook-Pro-3 ~ % afni
zsh: command not found: afni
laptop1@laptop1-MacBook-Pro-3 ~ %

Both the MNI and Talairach spaces have been widely used for adult human brain studies. The major differences are mostly caused by the use of atlases more closely related to the templates in these spaces. Note there are many versions of MNI and Talairach templates, so the template spaces vary quite a bit, and it's not enough to simply say a dataset is in one of these spaces; one should also say which template is used. In general, the MNI space templates are a little bigger than the Talairach versions, but the Talairach size is probably a little closer to the average size brain. Importantly, the Talairach space is originally defined on a stereotaxic procedure. There is no specific template that defines the Talairach space, unlike the MNI templates. We can follow the procedure, as we have for the N27 dataset, to put that into a Talairach space. Today, most atlases have been made for some version of an MNI template space, giving MNI spaces an important advantage.

https://afni.nimh.nih.gov/pub/dist/edu/latest/afni50_templates_atlases/afni50_templates_atlases.pdf