Hi all,
I am having trouble running sswarper2 with the push_to_edge option. This is the script I was trying to run:
sswarper2
-input $subj.anat.ac+orig
-base MNI152_2009_template_SSW.nii.gz
-subid $subj
-SSopt '-push_to_edge'
And this is the output I got:
** unexpected option #7 = '-SSopt'
Any help would be appreciated!
Gabby
Output of version check:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 3.10.0-1160.31.1.el7.x86_64
version: #1 SMP Thu Jun 10 13:32:12 UTC 2021
distribution: CentOS Linux 7.9.2009 Core
number of CPUs: 32
apparent login shell: bash (current shell is tcsh)
shell RC file: .cshrc (does not exist)
--------------------- AFNI and related program tests ---------------------
which afni : /opt/afni/24.1.16/afni
afni version : Precompiled binary linux_centos_7_64: May 30 2024
: AFNI_24.1.16 'Publius Septimius Geta'
AFNI_version.txt : AFNI_24.1.16, linux_centos_7_64, May 30 2024, official
which python : /usr/bin/python
python version : 2.7.5
which R :
instances of various programs found in PATH:
afni : 1 (/opt/afni/24.1.16/afni)
R : 0
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
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : FAILURE
R: Command not found.
()
** missing binary library 'libR.so' in program R_io.so
()
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
tcsh version : 6.18.01
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.
R RHOME : R: Command not found.
------------------------------ 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
-------------------------------- env vars --------------------------------
PATH = /opt/afni/24.1.16:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/home/gatencio/bin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
----------------------------- eval dot files -----------------------------
()
----------- AFNI $HOME files -----------
()
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- no .tcshrc, will create one as a follower of .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)
dot file test : want 4 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.tcshrc 0 0 0 1
.cshrc 1 0 1 0
.bashrc 1 0 1 0
------------------------------ 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 /opt/afni/24.1.16
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3
========================= summary, please fix: =========================
- just be aware: login shell 'bash', but our code examples use 'tcsh'
- shell tcsh: missing setup file .cshrc
- missing program: R
- failure under initial "AFNI and related program tests"
- 'afni' executable is owned by root
- AFNI programs show FAILURE
- missing binary library: libR.so
- missing R packages (see rPkgsInstall)
- python library matplotlib is required
(see AFNI install docs for details) - please run: cp /opt/afni/24.1.16/AFNI.afnirc ~/.afnirc
- please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- dot file test : want 4 modifications across 3 files:
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)