Hi,
I'm trying to view the voume data using SUMA with MNI152_T1_2009c teamplate
suma -spec std.141.MNI152_2009_both.spec -sv MNI152_2009_SurfVol.nii
The surface looks like this, sometimes the surface in both hemi are very bright. I've checked the viewer panel and the configurations for the both hemi were identical.
The brightness issue happens before "talk" to AFNI.
How can I sovle this issue?
Howdy-
Could you please copy+paste the output of the following:
afni_system_check.py -check_all
?
thanks,
pt
Hi PT,
Here's the output
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386 (uname -m == 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
number of CPUs: 16
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/icu/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 20 2024
: AFNI_24.2.03 'Macrinus'
AFNI_version.txt : AFNI_24.2.03, macos_10.12_local, Aug 20 2024, official
which python : /opt/anaconda3/bin/python
python version : 3.9.12
which R : /usr/local/bin/R
R version : R version 4.4.1 (x86_64-apple-darwin20)
instances of various programs found in PATH:
afni : 1 (/Users/icu/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/bin/R)
python : 1 (/opt/anaconda3/bin/python3.9)
python2 : 0
python3 : 3
/opt/anaconda3/bin/python3.9
/usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/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 : /bin/tcsh
tcsh version : 6.21.00
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: phia!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: gamm4!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: metafor!
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/anaconda3/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.5.2
++ module loaded: flask
module file : /opt/anaconda3/lib/python3.9/site-packages/flask/__init__.py
flask version : 1.1.2
** 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@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
/usr/local/bin/python3.9 (sym link to /usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/mni/bin:/opt/dcm2niix/bin:/opt/anaconda3/bin:/opt/anaconda3/condabin:/Applications/Sublime Text.app/Contents/SharedSupport/bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/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:/Users/icu/abin:/Users/icu/.local/bin:/Applications/workbench/bin_macosx64
PYTHONPATH (sub-shell) =
R_LIBS (sub-shell) =
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) = /Applications/freesurfer/lib/gcc/lib::/opt/X11/lib/flat_namespace
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 : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, 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 : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/icu/afni_global
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /usr/local/bin/brew
brew version : Homebrew 3.6.1
** consider linking /usr/local/Cellar/gcc/11.2.0_3/lib/gcc/11/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.72.0/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'zsh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib::/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* CPU differs between python and uname?
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
Best,
Xin
OK, @dglen has offered a suggestion (even whilst on holiday!): adjust the location of the light source. The default location of it is (0,0,1). Is it possible that dataset is far away from being centered around the coordinate origin?
If you open up SUMA and hover the mouse over the image window, and then type Shift+l (that is, like "capital L"), and enter a new coordinate location, does moving the light source fix the issue (or at least change the view)?
--pt
Thanks PT and Dan!
The problem cannot be reproduced when I load the same dataset this time. The brightness looks normal.
Very glad to know the shift+l shortcut! Exploring AFNI is so much fun!
Best,
Xin
Self-healing code is my favorite thing!
Thanks for letting us know.
--pt
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