Hello,
I am quite new to MRI data processing. I have preprocessed my resting state data with meica and now I would like to start with ROI-seeded correlation maps and functional connectivity analysis but I am having a hard time executing some of the scripts discussed in proc.py examples ( i.e. example 11b). I have about 28 patients that underwent TMS to the calcimine sulcus and I am now looking at post-stem resting state network changes. My questions:
1-Now that I preprocessed my data with meica, Is there a stepwise approach that I can follow for correlation maps (DMN & stimulation site) and functional connectivity analysis?
2- I know uber_subject.py is not recommended and I should learn to use the scripts but It might be a good start for me to at least learn the steps. Though for the life of me I cannot get it to work and I get the pesky "failed to import PyQt4.QtGui" error despite afni_system_check.py -check_all showing no issues with installation. (I tried setenv PYTHONPATH /usr/local/lib/python2.7/site-packages and no cigar!) I even tried installing ANACONDA and fink and pytq directly. The afni system check is pasted at the bottom.
3- How can I automate my resting state analysis-- group analysis (I heard in one of your videos someone said I can beg to see if somebody is willing to share their scripts with me)?
Thank you and happy new year!
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Tue Nov 10 00:10:30 PST 2020; root:xnu-6153.141.10~1/RELEASE_X86_64
distribution: 10.15.7
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/remycohan/abin/afni
afni version : Precompiled binary macos_10.12_local: Dec 22 2020
: AFNI_20.3.04 'Vespasian'
AFNI_version.txt : AFNI_20.3.04, macos_10.12_local, Dec 22 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/remycohan/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3
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 : success
R RHOME : /Library/Frameworks/R.framework/Resources
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
++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
/usr/local/bin/python3.9 (sym link to /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/3.9/bin:/usr/local/opt/qt/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/remycohan/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/remycohan/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.7.0
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /usr/bin/python
** consider linking /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgomp.1.dylib under /usr/local/lib
-- consider installing glib under homebrew
++ 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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= nothing to fix, yay! =========================
