Hi experts,
I am currently working on an analysis using AFNI, and I have encountered an error during the preprocessing stage. Below are the details of the issue:
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_FR-T1-1R+orig -prefix ./__tt_FR-T1-1R_ns
Fatal Signal 11 (SIGSEGV) received
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_20.3.01 Compile date = Oct 19 2020
** [[Precompiled binary linux_centos_7_64: Oct 19 2020]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/rshuang/.afni.crashlog
** ERROR: Could not strip skull
** ERROR - script failed
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++find_filename_extension [4]: {ENTRY (file=thd_opendset.c line=674) from SUMA_ParseFname_eng {1 ms}
----find_filename_extension [4]: EXIT} (file=thd_opendset.c line=683) to SUMA_ParseFname_eng {1 ms}
++++SUMA_copy_string [4]: {ENTRY (file=suma_utils.c line=2543) from SUMA_ParseFname_eng {1 ms}
----SUMA_copy_string [4]: EXIT} (file=suma_utils.c line=2556) to SUMA_ParseFname_eng {1 ms}
++++SUMA_copy_string [4]: {ENTRY (file=suma_utils.c line=2543) from SUMA_ParseFname_eng {1 ms}
----SUMA_copy_string [4]: EXIT} (file=suma_utils.c line=2556) to SUMA_ParseFname_eng {1 ms}
++++SUMA_copy_string [4]: {ENTRY (file=suma_utils.c line=2543) from SUMA_ParseFname_eng {1 ms}
----SUMA_copy_string [4]: EXIT} (file=suma_utils.c line=2556) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_string [4]: {ENTRY (file=suma_utils.c line=2735) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_string [4]: EXIT} (file=suma_utils.c line=2766) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_string [4]: {ENTRY (file=suma_utils.c line=2735) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_string [4]: EXIT} (file=suma_utils.c line=2766) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
++++SUMA_append_replace_string_eng [4]: {ENTRY (file=suma_utils.c line=2806) from SUMA_ParseFname_eng {1 ms}
----SUMA_append_replace_string_eng [4]: EXIT} (file=suma_utils.c line=2871) to SUMA_ParseFname_eng {1 ms}
---SUMA_ParseFname_eng [3]: EXIT} (file=suma_utils.c line=1439) to SUMA_SetAutoRecord {1 ms}
--SUMA_SetAutoRecord [2]: EXIT} (file=SUMA_SVmanip.c line=4594) to Bottom of Debug Stack {1 ms}
++3dSkullStrip [2]: {ENTRY (file=SUMA_3dSkullStrip.c line=1357) from Bottom of Debug Stack {1 ms}
............................................................................
3dSkullStrip
** AFNI compile date = Oct 19 2020
** [[Precompiled binary linux_centos_7_64: Oct 19 2020]]
** Program Crash **
when i input afni_system_check.py -check_all, the output is that:
rshuang@90.1:/RAID/fspace/FJW/image>afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.18.0-240.10.1.el8_3.x86_64
version: #1 SMP Mon Jan 18 17:05:51 UTC 2021
distribution: CentOS Linux 8
number of CPUs: 64
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/rshuang/AFNI/afni
afni version : Precompiled binary linux_centos_7_64: Oct 19 2020
: AFNI_20.3.01 'Vespasian'
AFNI_version.txt : AFNI_20.3.01, linux_centos_7_64, Oct 19 2020
which python : /home/packages/fsl/fslpython/bin/python
python version : 3.9.16
which R : which: no R in (/home/packages/fsl/bin:/usr/sbin:/sbin:/usr/bin:/usr0/bin:/usr/bin/X11:/bin:/etc:/usr/etc:/home/rshuang/bin:/home/rshuang/AFNI:/home/packages/R2019a/bin:/home/packages/fsl/bin:/home/packages/fsl/fslpython/bin:/home/rshuang/csurf/bin/noarch/:/home/rshuang/csurf/bin/Linux-x86_64:/usr/local/bin:/usr/local/lib:/usr/local/pbmplus/bin:.)
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/rshuang/AFNI/afni)
R : 0
python : 2
/home/rshuang/.local/bin
/home/packages/fsl/fslpython/bin/python3.9
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/usr/libexec/platform-python3.6
/home/packages/fsl/fslpython/bin/python3.9
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : FAILURE
Fatal Signal 11 (SIGSEGV) received
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_20.3.01 Compile date = Oct 19 2020
** [[Precompiled binary linux_centos_7_64: Oct 19 2020]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/rshuang/.afni.crashlog
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.
R RHOME : R: Command not found.
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 : /home/packages/fsl/fslpython/lib/python3.9/site-packages/matplotlib/pyplot.py
-------------------------------- env vars --------------------------------
PATH = /home/packages/fsl/bin:/usr/sbin:/sbin:/usr/bin:/usr0/bin:/usr/bin/X11:/bin:/etc:/usr/etc:/home/rshuang/bin:/home/rshuang/AFNI:/home/packages/R2019a/bin:/home/packages/fsl/bin:/home/packages/fsl/fslpython/bin:/home/rshuang/csurf/bin/noarch/:/home/rshuang/csurf/bin/Linux-x86_64:/usr/local/bin:/usr/local/lib:/usr/local/pbmplus/bin:.
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /home/rshuang/AFNI/
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 /home/rshuang/AFNI
------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.7.0
which yum : /usr/bin/yum
yum version : 4.7.0
========================= summary, please fix: =========================
- failure under initial "AFNI and related program tests"
- AFNI programs show FAILURE
- missing R packages (see rPkgsInstall)
- insufficient data for AFNI bootcamp