Hi, Robin-
I am going to split this into a new thread, as it is a separate question from here (where it was originally posted):
[
afni.nimh.nih.gov]
I have also edited the subject line to reflect the first error shown in the output.
Hope that is all reasonable.
(Heading into work now, will reply more anon, or perhaps someone else will chime in first.)
-pt
---------------------------------------------------------------------------
Sorry but it seems we have a new error post update...
This is the output of afni_system_check -check_all
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_openmp_64: Feb 14 2020
: AFNI_20.0.09 'Galba'
AFNI_version.txt : AFNI_20.0.09, linux_openmp_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
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- 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
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* please run: cp /usr/local/abin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* insufficient data for AFNI bootcamp
When running 2 diferent pre-procs 1) Old one on old data that worked before and 2) A new analysis with updated pre-proc and new data we get FATAL ERRORs. This is on both of our Ubuntu 16 and Ubuntu18.
Pre-proc1)
-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/* \
Output error of pre-proc 1:
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'
Pre-proc2)
-blocks despike tshift align tlrc volreg mask regress \
-align_opts_aea \
-giant_move \
-tcat_remove_first_trs 0 \
-volreg_align_to MIN_OUTLIER \
-tlrc_NL_warp \
-volreg_tlrc_warp \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_stim_types AM1 \
-regress_basis 'dmBLOCK' \
-regress_stim_times $stim/* \
Output error pre-proc 2:
Performing center alignment with @Align_Centers
++ 3dcopy: AFNI version=AFNI_20.0.09 (Feb 14 2020) [64-bit]
++ 3drefit: AFNI version=AFNI_20.0.09 (Feb 14 2020) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
+ deoblique
++ 3drefit processed 1 datasets
else: endif not found.
ls: cannot access 'anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft.1D': No such file or directory
** ERROR: mri_matrix_evalrpn('&read4x4Xform() &write(stdout:) ') at '&read4x4Xform()': can't read file ''
mv: missing destination file operand after 'anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_44.1D'
Try 'mv --help' for more information.
++ 3drename: AFNI version=AFNI_20.0.09 (Feb 14 2020) [64-bit]
++ THD_rename_dataset_files: rename anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK -> __ats_tmp__anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK
** THD_rename_dataset_files: old header anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
if: Missing file name.
#**ERROR Failed in affine step
** ERROR - script failed
With the afni_system_check output beeing good(?) I'm a bit confused?
Edited 1 time(s). Last edit at 02/18/2020 08:32AM by ptaylor.
