Hi beautiful AFNI people!
I had the pleasure to attend your LIBR bootcamp earlier this month... just in time I guess.
Would you mind having a look at two questions?
1) I'm setting up some resting-state data for preprocessing with the help of Example 11 of the afni_proc.py help.
It is suggested to use check_dsets_for_fs.py to prepare the data before running Freesurfers recon_all.
If I understand your update, Paul, correctly this is not necessary at all anymore? Is that true only for a certain (new) Freesurfer version or just a general conclusion?
So can I just mri_convert my data from BRIK to mgz and proceed accordingly with recon_all?
I'm referring to this update:
12 Mar 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL)
This program has been deemed unnecessary.
Also the afni_proc.py help suggests now using @SSwarper's skull stripping instead of Freesurfers.
Does this mean I just add the -<no>skullstrip option to the recon_all program and change the -anat_has_skull option to 'yes' in afni_proc.py?
2) I use AFNI on Windows Subsystem for Linux (shame on me, I know).
Whenever I use the "whereami" option in the AFNI GUI to determine where the heck I'm at in a brain the program crashes without an error message.
Find my afni_system_check.py -check_all log attached. Any ideas on that?
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.4.0-18362-Microsoft
version: #1-Microsoft Mon Mar 18 12:02:00 PST 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/jonas/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Feb 26 2020
: AFNI_20.0.18 'Galba'
AFNI_version.txt : AFNI_20.0.18, linux_ubuntu_16_64, Feb 26 2020
which python : /usr/bin/python
python version : 2.7.17
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/jonas/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)
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.UbuntuonWindows_1804.2020.5.0_x64__79rhkp1fndgsc:/mnt/c/Program Files/Python38/Scripts/:/mnt/c/Program Files/Python38/:/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/PuTTY/:/mnt/c/Users/JSteinhauser/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/JSteinhauser/AppData/Local/Programs/Microsoft VS Code/bin:/snap/bin:/home/jonas/abin
PYTHONPATH =
R_LIBS = /home/jonas/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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: 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/jonas/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.10 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Feb 26 2020
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .profile
Thanks a lot for your help and the awesome bootcamp.
You guys rock!
Best regards,
Jonas
Edited 1 time(s). Last edit at 03/18/2020 04:39PM by Jonas_St.
