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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| November 20, 2019 02:51AM | |
Registered: 4 years ago Posts: 2 |
Hello,
I'm having some trouble installing AFNI. I'm running Ubuntu in a terminal in Windows 10. I'm also a beginner to both AFNI and Unix/Linux.
Here is the output for rPkgsInstall -pkgs ALL
Meanwhile, I have tried
the initial interface is this
I'd appreciate if you give any suggestions I can do!!!
Thank you very much!
I'm having some trouble installing AFNI. I'm running Ubuntu in a terminal in Windows 10. I'm also a beginner to both AFNI and Unix/Linux.
Here is the output for rPkgsInstall -pkgs ALL
-------------------------------- general --------------------------------- architecture: 64bit ELF system: Linux release: 4.4.0-17763-Microsoft version: #864-Microsoft Thu Nov 07 15:22:00 PST 2019 distribution: Ubuntu 16.04 xenial number of CPUs: 8 apparent login shell: bash shell RC file: .bashrc (exists) --------------------- AFNI and related program tests --------------------- which afni : /home/bo/abin/afni afni version : Precompiled binary linux_ubuntu_16_64: Aug 29 2019 : AFNI_19.2.21 'Claudius' AFNI_version.txt : AFNI_19.2.21, linux_ubuntu_16_64, Aug 29 2019 which python : /usr/bin/python python version : 2.7.12 which R : /usr/bin/R R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes" which tcsh : /usr/bin/tcsh instances of various programs found in PATH: afni : 1 (/home/bo/abin/afni) R : 1 (/usr/bin/R) python : 1 (/usr/bin/python2.7) python2 : 1 (/usr/bin/python2.7) python3 : 1 (/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 : success R RHOME : /usr/lib/R checking for $HOME files... .afnirc : found .sumarc : found .afni/help/all_progs.COMP : found ------------------------------ python libs ------------------------------- ++ module loaded: PyQt4 module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc ** failed to load module matplotlib.pyplot -- matplotlib.pyplot is not required, but is desirable -------------------------------- env vars -------------------------------- PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu16.04onWindows_1604.2019.523.0_x64__79rhkp1fndgsc:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/iCLS:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/iCLS:/mnt/c/Windows/System32:/mnt/c/Windows:/mnt/c/Windows/System32/wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Users/bochao/AppData/Local/Microsoft/WindowsApps:/mnt/c/Program Files/Bandizip:/snap/bin:/home/bo/abin:/home/bo/abin:/home/bo/abin:/home/bo/abin:/home/bo/abin:/home/bo/abin PYTHONPATH = R_LIBS = /home/bo/R LD_LIBRARY_PATH = DYLD_LIBRARY_PATH = DYLD_FALLBACK_LIBRARY_PATH = ------------------------------ data checks ------------------------------- data dir : found AFNI_data6 under $HOME top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05 data dir : found AFNI_demos under $HOME top history: 22 Oct 2019 [discoraj]: added Cluster Explorer 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 $HOME atlas : found TT_N27+tlrc under /home/bo/abin ------------------------------ OS specific ------------------------------- which apt-get : /usr/bin/apt-get apt-get version : apt 1.2.31 (amd64) have Ubuntu system: Ubuntu 16.04 xenial have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Aug 29 2019 ========================= summary, please fix: ========================= * login shell 'bash', trusting user to translate code examples from 'tcsh' bo@DESKTOP-MRDNLP6:~$ grep bionic /etc/apt/sources.list bo@DESKTOP-MRDNLP6:~$ afni_system_check.py -check_all -------------------------------- general --------------------------------- architecture: 64bit ELF system: Linux release: 4.4.0-17763-Microsoft version: #864-Microsoft Thu Nov 07 15:22:00 PST 2019 distribution: Ubuntu 16.04 xenial number of CPUs: 8 apparent login shell: bash shell RC file: .bashrc (exists) --------------------- AFNI and related program tests --------------------- which afni : /home/bo/abin/afni afni version : Precompiled binary linux_ubuntu_16_64: Aug 29 2019 : AFNI_19.2.21 'Claudius' AFNI_version.txt : AFNI_19.2.21, linux_ubuntu_16_64, Aug 29 2019 which python : /usr/bin/python python version : 2.7.12 which R : /usr/bin/R R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes" which tcsh : /usr/bin/tcsh instances of various programs found in PATH: afni : 1 (/home/bo/abin/afni) R : 1 (/usr/bin/R) python : 1 (/usr/bin/python2.7) python2 : 1 (/usr/bin/python2.7) python3 : 1 (/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 : success R RHOME : /usr/lib/R checking for $HOME files... .afnirc : found .sumarc : found .afni/help/all_progs.COMP : found ------------------------------ python libs ------------------------------- ++ module loaded: PyQt4 module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc ** failed to load module matplotlib.pyplot -- matplotlib.pyplot is not required, but is desirable -------------------------------- env vars -------------------------------- PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu16.04onWindows_1604.2019.523.0_x64__79rhkp1fndgsc:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/iCLS:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/iCLS:/mnt/c/Windows/System32:/mnt/c/Windows:/mnt/c/Windows/System32/wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Users/bochao/AppData/Local/Microsoft/WindowsApps:/mnt/c/Program Files/Bandizip:/snap/bin:/home/bo/abin:/home/bo/abin:/home/bo/abin:/home/bo/abin:/home/bo/abin:/home/bo/abin PYTHONPATH = R_LIBS = /home/bo/R LD_LIBRARY_PATH = DYLD_LIBRARY_PATH = DYLD_FALLBACK_LIBRARY_PATH = ------------------------------ data checks ------------------------------- data dir : found AFNI_data6 under $HOME top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05 data dir : found AFNI_demos under $HOME top history: 22 Oct 2019 [discoraj]: added Cluster Explorer 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 $HOME atlas : found TT_N27+tlrc under /home/bo/abin ------------------------------ OS specific ------------------------------- which apt-get : /usr/bin/apt-get apt-get version : apt 1.2.31 (amd64) have Ubuntu system: Ubuntu 16.04 xenial have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Aug 29 2019 ========================= summary, please fix: ========================= * login shell 'bash', trusting user to translate code examples from 'tcsh' bo@DESKTOP-MRDNLP6:~$
Meanwhile, I have tried
echo "" >> ~/.bash_profile echo "source ~/.bashrc" >> ~/.bash_profile echo "" >> ~/.bash_profilethe AFNI still does't work.
the initial interface is this
Precompiled binary linux_ubuntu_16_64: Aug 29 2019 (Version AFNI_19.2.21 'Claudius') ** Version check disabled: AFNI_VERSION_CHECK forbids Thanks go to V Roopchansingh for great efforts Initializing: X11Error: Can't open display: ++ AFNI is detached from terminal.
I'd appreciate if you give any suggestions I can do!!!
Thank you very much!
| Subject | Author | Posted |
|---|---|---|
|
bochao | November 20, 2019 02:51AM |
|
ptaylor | November 20, 2019 08:45AM |
|
bochao | November 20, 2019 10:16AM |
|
ptaylor | November 20, 2019 10:25AM |
