This project forked from fristed/beast
C implementation of Brain Extraction based on nonlocal Segmentation Technique
Home Page: http://www.bic.mni.mcgill.ca/BEaST
License: GNU General Public License v3.0
I am having trouble running beast_normalize on my dataset. I am using minc-toolkit-v2 1.9.16 installed with the supplied singularity container. The command I am running is:
singularity exec ~/singularity/minc-toolkit-1.9.16.simg \
beast_normalize head.mnc head_mni.mnc tmp/anat2mni.xfm \
-modeldir /opt/minc/share/icbm152_model_09c
After the "Transforming slices..." step, it exits with the message:
No points were chosen by the specified criteria
resample_labels: crashed while running extracttag (termination status=256)
nu_estimate_np_and_em: crashed while running resample_labels (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
I have attached an example image file that I am using; the scan is derived from a scan in the public domain: TCIA-GBM collection (subject TCGA-12-3650).
How can I debug? Given that it happens with all scans in my database, this must either be a problem with my install or the dataset I am using but I am at a loss as to progress further. I would be grateful for any advice.
I just built BEaST and noticed that the #!/bin/bash line is not at the correct (first line) position in the beast_normalize and beast_prepareADNIlib files (I'm running the fish shell in my terminals - that's why I noticed this issue).
Running in a script with "set -e" to stop immediately on error:
Writing a binary volume...
Error creating HDF file '/tmp/tmp.wdSGm0Jpu9/beastmask0.mnc' with mode '2', result -1
HDF5-DIAG: Error detected in HDF5 (1.8.15-patch1) thread 0:
#000: /opt/quarantine/minc-toolkit/1.9.11/src/build/HDF5/src/H5F.c line 522 in H5Fcreate(): unable to create file
major: File accessibilty
minor: Unable to open file
#001: /opt/quarantine/minc-toolkit/1.9.11/src/build/HDF5/src/H5Fint.c line 1001 in H5F_open(): unable to open file: time = Thu Dec 1 16:45:32 2016
, name = '/tmp/tmp.wdSGm0Jpu9/beastmask0.mnc', tent_flags = 13
major: File accessibilty
minor: Unable to open file
#002: /opt/quarantine/minc-toolkit/1.9.11/src/build/HDF5/src/H5FD.c line 993 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: /opt/quarantine/minc-toolkit/1.9.11/src/build/HDF5/src/H5FDsec2.c line 343 in H5FD_sec2_open(): unable to open file: name = '/tmp/tmp.wdSGm0Jpu9/beastmask0.mnc', errno = 13, error message = 'Permission denied', flags = 13, o_flags = 242
major: File accessibilty
minor: Unable to open file
(from micreate): Unable to create file '/tmp/tmp.wdSGm0Jpu9/beastmask0.mnc'
Error: opening MINC file "/tmp/tmp.wdSGm0Jpu9/beastmask0.mnc".
Script continued to run.
Same symptoms as NIST-MNI/patch_morphology#4
Same solution.
I guess points to minc-toolkit-v2 superbuild issue.
The minc tool kit that I install with command ('dpkg -i .deb') is located in /opt/minc/1.9.16 (1.9.16 is the version). However, in the beast_prepareADNIlib line 61, it tries to locate 'minc-toolkit-config.sh' under /opt/minc/, but couldn't find it. I can adapt it to my code, but I feel it is desirable to have a more general way to do that.
testing files used to be at https://www.bic.mni.mcgill.ca/~vfonov/temp/beast-testing-1.0.tar.gz
Now missing :)
The "sparse" test files seem to be missing (e.g., /test_2_v1_sparse_single.mnc).
I got a pragma error on beast while compiling beast with the minc toolkit v2
On fedora 23
icpc --version
icpc (ICC) 15.0.3 20150407
Copyright (C) 1985-2015 Intel Corporation. All rights reserved.
minc/minc-toolkit-v2/BEaST/nlmsegFuzzy.c(271): error: invalid parallel pragma
#pragma parallel for reduction(+:count)
... And just commented the line.
If OpenMP isn't found, a warning is emitted:
https://github.com/BIC-MNI/BEaST/blob/develop/CMakeLists.txt#L97-L106
But there are ifdefs everywhere which will still compile-in openmp calls.
This is my remaining bug for 32bit Centos6, where OpenMP is either broken or cmake can't find it properly:
35781 -- Could NOT find OpenMP_C (missing: OpenMP_pthread_LIBRARY) (found version "3.1")
35782 -- Could NOT find OpenMP_CXX (missing: OpenMP_pthread_LIBRARY) (found version "3.1")
35783 -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
35784 CMake Warning at CMakeLists.txt:104 (message):
35785 OpenMP NOT found
And then a linking error because the omp_thread calls were still in the code:
36035 [ 94%] Building CXX object CMakeFiles/mincbeast.dir/mincbeast.o
36036 [100%] Linking CXX executable mincbeast
36037 CMakeFiles/mincbeast.dir/mincbeast.o: In function `main':
36038 mincbeast.cpp:(.text.startup+0x30): undefined reference to `omp_get_max_threads'
36039 libbeast.a(beast_lib.o): In function `median_filter(float*, int*, int)':
36040 beast_lib.cpp:(.text+0x126): undefined reference to `omp_get_max_threads'
36041 beast_lib.cpp:(.text+0x141): undefined reference to `omp_get_max_threads'
36042 beast_lib.cpp:(.text+0x1b2): undefined reference to `omp_get_thread_num'
36043 beast_lib.cpp:(.text+0x409): undefined reference to `omp_get_max_threads'
36044 libbeast.a(nlmsegFuzzy.o): In function `nlmsegFuzzy4D(float const*, float const*, float const*, float const*, float const*, float const*, int, int, float, float, int const*, int, float*, float*)':
36045 nlmsegFuzzy.cpp:(.text+0x14): undefined reference to `omp_get_max_threads'
36046 nlmsegFuzzy.cpp:(.text+0x2b): undefined reference to `omp_get_max_threads'
36047 nlmsegFuzzy.cpp:(.text+0x42): undefined reference to `omp_get_max_threads'
36048 nlmsegFuzzy.cpp:(.text+0x13d): undefined reference to `omp_get_max_threads'
36049 libbeast.a(nlmsegFuzzy.o):nlmsegFuzzy.cpp:(.text+0x362): more undefined references to `omp_get_max_threads' follow
36050 libbeast.a(nlmsegFuzzy.o): In function `nlmsegFuzzy4D(float const*, float const*, float const*, float const*, float const*, float const*, int, int, float, float, int const*, int, float*, float*)':
36051 nlmsegFuzzy.cpp:(.text+0x3b3): undefined reference to `omp_get_thread_num'
36052 nlmsegFuzzy.cpp:(.text+0x3bf): undefined reference to `omp_get_num_threads'
36053 nlmsegFuzzy.cpp:(.text+0x3ec): undefined reference to `omp_get_thread_num'
36054 nlmsegFuzzy.cpp:(.text+0x3ff): undefined reference to `omp_get_thread_num'
36055 nlmsegFuzzy.cpp:(.text+0x412): undefined reference to `omp_get_thread_num'
36056 nlmsegFuzzy.cpp:(.text+0xb9b): undefined reference to `omp_get_max_threads'
36057 nlmsegFuzzy.cpp:(.text+0xc8b): undefined reference to `omp_get_max_threads'
36058 libbeast.a(nlmsegFuzzy.o): In function `nlmsegFuzzy4D_double(float const*, float const*, float const*, float const*, float const*, float const*, int, int, double, double, int const*, int, float*, float*)':
36059 nlmsegFuzzy.cpp:(.text+0xd8d): undefined reference to `omp_get_max_threads'
36060 nlmsegFuzzy.cpp:(.text+0xda4): undefined reference to `omp_get_max_threads'
36061 nlmsegFuzzy.cpp:(.text+0xdbb): undefined reference to `omp_get_max_threads'
36062 libbeast.a(nlmsegFuzzy.o):nlmsegFuzzy.cpp:(.text+0xeb3): more undefined references to `omp_get_max_threads' follow
36063 libbeast.a(nlmsegFuzzy.o): In function `nlmsegFuzzy4D_double(float const*, float const*, float const*, float const*, float const*, float const*, int, int, double, double, int const*, int, float*, float*)':
36064 nlmsegFuzzy.cpp:(.text+0x1129): undefined reference to `omp_get_thread_num'
36065 nlmsegFuzzy.cpp:(.text+0x1135): undefined reference to `omp_get_num_threads'
36066 nlmsegFuzzy.cpp:(.text+0x1162): undefined reference to `omp_get_thread_num'
36067 nlmsegFuzzy.cpp:(.text+0x1178): undefined reference to `omp_get_thread_num'
36068 nlmsegFuzzy.cpp:(.text+0x118b): undefined reference to `omp_get_thread_num'
36069 nlmsegFuzzy.cpp:(.text+0x1927): undefined reference to `omp_get_max_threads'
36070 nlmsegFuzzy.cpp:(.text+0x1a14): undefined reference to `omp_get_max_threads'
36071 collect2: error: ld returned 1 exit status
When compiling with 9.1.1 (Fedora) the tests fail with a segmentation fault. This does not occur with older versions of gcc (4.8.5 Centos7). It also does not occur when compiling in debug mode. I started doing some digging, and I believe the error occurs during argument parsing, due to this issue.
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