Hi and thanks!
I did screw up, I pasted my previous installation command and that was on a CentOS system. I removed the abin directory completely, downloaded the source from
here due to proxy-issues. Then I went to my local home-folder and ran
curl -O [afni.nimh.nih.gov]
Followed by
tcsh @update.afni.binaries -local_package /home/robka/linux_ubuntu_16_64.tgz -do_extras -bindir /usr/local/abin
Unfortunately the problem persists.
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.2 LTS
Release: 18.04
Codename: bionic
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.15.0-51-generic
version: #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Feb 14 2020
: AFNI_20.0.09 'Galba'
AFNI_version.txt : AFNI_20.0.09, linux_ubuntu_16_64, Feb 14 2020
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/usr/local/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 : missing
.sumarc : missing
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python2.7/dist-packages/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/home/robka/.local/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/abin:/usr/local/MATLAB/R2015b/bin:/usr/local/mricron_lx:/usr/local/xnat_img_download:/usr/local/stim_file_gen:/usr/local/mricron_old:/usr/local/xnat_resource_downloader:/opt/thinlinc/bin:/usr/local/abin:/usr/local/abin
PYTHONPATH = /usr/local/pylib_shared
R_LIBS = /usr/lib/R
LD_LIBRARY_PATH = /usr/lib/x86_64-linux-gnu/
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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 /usr/local/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.11 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Feb 14 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
* please run: cp /usr/local/abin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* insufficient data for AFNI bootcamp
Proc-Blocks
-blocks despike tshift align tlrc volreg mask scale regress \
-mask_segment_anat yes \
-mask_segment_erode yes \
-tshift_opts_ts -tpattern seq+z \
-align_opts_aea -ginormous_move -deoblique on -cost lpc+zz \
-tcat_remove_first_trs 0 \
-tlrc_base MNI_avg152T1+tlrc \
-volreg_tlrc_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_stim_types AM1 \
-regress_basis 'dmBLOCK' \
-regress_stim_times $stim/* \
Error-Output
3dSkullStrip -orig_vol -input ./__tt_T1+orig -prefix ./__tt_T1_ns
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_T1+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_T1+orig.BRIK is 4.693148 degrees from plumb.
#Script is running (command trimmed):
3dinfo ./__tt_T1_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /fenix/users/irepe/scn9a/M_sub01_run1.results/__tt_T1_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./vr_base_min_outlier+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /fenix/users/irepe/scn9a/M_sub01_run1.results/vr_base_min_outlier+orig is ***oblique****
#Script is running:
3dAttribute DELTA /fenix/users/irepe/scn9a/M_sub01_run1.results/__tt_T1_ns+orig
#++ Spacing for anat to oblique epi alignment is 0.868056
#Script is running (command trimmed):
3dcopy ./__tt_T1_ns+orig ./__tt_T1_ns_ob; @Align_Centers -base ./vr_base_min_outlier+orig -dset ./__tt_T1_ns_ob+orig -no_cp
++ 3dcopy: AFNI version=AFNI_20.0.09 (Feb 14 2020) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 8.172770 degrees from plumb.
++ 3drefit: AFNI version=AFNI_20.0.09 (Feb 14 2020) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./__tt_T1_ns_ob+orig
+ deoblique
++ 3drefit processed 1 datasets
else: endif not found.
#Script is running (command trimmed):
cat_matvec ./__tt_T1_ns_ob_shft.1D -I > ./__tt_T1_ns_shft_I.1D
** ERROR: mri_read_double_ascii: couldn't open file ./__tt_T1_ns_ob_shft.1D
** ERROR: THD_read_dvecmat: can't read matrix+vector from './__tt_T1_ns_ob_shft.1D'
** FATAL ERROR: Can't read matrix from './__tt_T1_ns_ob_shft.1D'
It would have made so much sense if installing the correct binaries solved this problem...
