Thank you kindly Rick!
I have made some progress, though are still some problems, and i presume they are to do with a lack of installed packages.
I wonder if the 1 missing R package is substantial?
I wish to use the @SSwarper command in addition to:
"afni_proc.py \
-subj_id # enter your subject and directory of it here \
-out_dir # enter your output directory... for the results here \
-dsets \
# enter EPI/functional raw scan here \
-blocks despike tshift align tlrc volreg mask blur regress \
-copy_anat $directory_sswarper_1/anatSS.$subject.nii \
-anat_has_skull no \
-tcat_remove_first_trs 4 \
-align_opts_aea -cost lpc+ZZ \ # lpc+ZZ is a standard... you can try this first
-volreg_align_e2a \
-volreg_align_to MIN_OUTLIER \
-volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
$directory_sswarper_1/anatQQ.$subject.nii \ # please enter the specific subject files here...
$directory_sswarper_1/anatQQ.$subject.aff12.1D \
$directory_sswarper_1/anatQQ.${subject}_WARP.nii \
-volreg_post_vr_allin yes \
-volreg_pvra_base_index MIN_OUTLIER \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_anaticor \
-regress_ROI WMe CSFe \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_censor_motion 0.2 \ # please adjust... (0.2 is standard in afni for resting-state, but its up to you)
-regress_censor_outliers 0.05 \ # please adjust... (0.05 is standard in afni for resting-state, but its up to you)
-blur_size 8.0 \ # please adjust...
-regress_est_blur_epits \
-regress_est_blur_errts \
-html_review_style pythonic \
-execute"
Here is the current output from afni_system_check.py -check_all:
[coopapap@beluga1 ~]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type:
system: Linux
release: 3.10.0-1160.76.1.el7.x86_64
version: #1 SMP Wed Aug 10 16:21:17 UTC 2022
distribution: CentOS Linux 7 (Core)
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/coopapap/AFNIbin/afni
afni version : Precompiled binary linux_centos_7_64: Feb 13 2023
: AFNI_23.0.04 'Commodus'
AFNI_version.txt : AFNI_23.0.04, linux_centos_7_64, Feb 13 2023
which python : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python
python version : 3.8.10
which R : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/bin/R
R version : R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
which tcsh : /cvmfs/soft.computecanada.ca/gentoo/2020/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/coopapap/AFNIbin/afni)
R : 2
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/bin/R
/home/coopapap/R
python : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python2 : 2
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/usr/bin/python2.7
python3 : 3
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin/python3.8
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/python-exec2c
/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 : FAILURE
oo Warning:
These packages are not installed on the computer: brms!
R RHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/lib64/R
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 : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.2.1
-------------------------------- env vars --------------------------------
PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/gsl/1.16/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/scipy-stack/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/ipykernel/2020a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/fsl/6.0.3/fsl/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/wxwidgets/3.1.4/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/expat/2.2.9/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/jbigkit/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/qt/5.12.8/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/vtk/8.2.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/libgd/2.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/gcc9/cuda11.0/openmpi/4.0.3/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/libfabric/1.10.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/ucx/1.8.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/CUDA/cuda11.0/gdrcopy/2.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/nvvm/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/tktools:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/mni/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/fsfast/bin:/home/coopapap/.local/easybuild/software/2020/Core/freesurfer/6.0.1/bin:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5:/cvmfs/restricted.computecanada.ca/easybuild/software/2020/Core/matlab/2021a.5/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/mii/1.1.2/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin:/cvmfs/soft.computecanada.ca/custom/bin/computecanada:/home/coopapap:/home/coopapap/AFNIbin:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/r/4.0.2/bin/R:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/coopapap/.local/bin:/home/coopapap/bin
PYTHONPATH = /cvmfs/soft.computecanada.ca/easybuild/python/site-packages:/cvmfs/soft.computecanada.ca/custom/python/site-packages
R_LIBS = /home/coopapap/R
LD_LIBRARY_PATH = /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/gsl/1.16/lib
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered opertaions: path, flatdir, apsearch
(not on a mac, should skip flatdir)
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 2 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 1 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (109595417M Avail)
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 /home/coopapap/AFNIbin
------------------------------ 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'
* missing R packages (see rPkgsInstall)
* dot file test : want 2 modifications across 3 files:
Edited 1 time(s). Last edit at 02/21/2023 05:39PM by coopapap.
