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Author Topic: Some problems with running tt_demo_... ?!
shahrokh
Newbie
Posts: 5
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Post Some problems with running tt_demo_... ?!
on: December 6, 2016, 13:10
Quote

Hello Dear NiftyRec Developers,

I think that I installed niftyrec (NiftyRec-2.3.2.zip) on fedora core 22 (as mentioned below) with MATLAB 2015b.
[sn@localhost ~]$ uname --all
Linux localhost.localdomain 4.0.4-301.fc22.x86_64 #1 SMP Thu May 21 13:10:33 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
[sn@localhost ~]$

I install NiftyRec-2.3.2 with the following commands:
[sn@localhost ~]$ mkdir ./niftyrec/
[sn@localhost ~]$ cd ./niftyrec/
[sn@localhost niftyrec]$ unzip NiftyRec-2.3.2.zip
...
[sn@localhost niftyrec]$ ll -h
[sn@localhost niftyrec]$ mkdir /home/sn/niftyrec-build
[sn@localhost niftyrec]$ sudo mkdir /usr/local/niftyrec
[sn@localhost niftyrec]$ cd /home/sn/niftyrec-build
[sn@localhost niftyrec-build]$ ccmake /home/sn/niftyrec/NiftyRec-2.3.2
...
Press [c] to configure
...
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /usr/local/niftyrec
MATLAB_INCLUDE /usr/local/MATLAB/R2015b/extern/include
MATLAB_LIBS_DIR /usr/local/MATLAB/R2015b/bin/glnxa64
NiftyRec_BUILD_APPS ON
NiftyRec_BUILD_MATLAB ON
NiftyRec_BUILD_RENDERER OFF
NiftyRec_COMPILE_DOC OFF
NiftyRec_INCLUDE_DATA ON
NiftyRec_SUPPORT_NRRD OFF
NiftyRec_USE_CUDA OFF
NiftyRec_USE_OPENMP ON
NiftyRec_VERBOSE OFF
Press [g] to generate
[sn@localhost niftyrec-build]$ make
[sn@localhost niftyrec-build]$ su
Password:
[root@localhost niftyrec-build]# make install
...
[root@localhost niftyrec-build]#

At now, I add the variable of LD_LIBRARY_PATH to /home/sn/.bashrc file as mentioned below line:
...
# niftyrec
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/niftyrec/lib/
...
In new terminal, I run matlab and add the path of "/usr/local/niftyrec/niftyrec/matlab" in "Set Path" icon of matlab and
At now, I can run et_demo_osem successfully. :D

My problems are started in here. I want to construct 3-D images from EPID images acquired with LINAC using niftyrec. For this purpose and start this project, I want to run demos of tt such as tt_demo_mlem_conebeam and tt_demo_mlem_parallel.
When I run tt_demo_mlem_conebeam, I get the following error message:
>> tt_demo_mlem_conebeam
Undefined function or variable 'tt_project_ray_mex'.

Error in tt_demo_mlem_conebeam (line 69)
p =
tt_project_ray_mex(attenuation,volume_size_mm,source_location_mm,int32(detector_size_pix),detector_size_mm,detector_translation_mm,detector_rotation_rad,ray_step_vox);

>>
Also when I run tt_demo_mlem_parallel_large, I get the following huge error message and crash MATLAB:
>> tt_demo_mlem_parallel_large
Loading phantom ...
Padding ...
Rotating ...
Cropping ...
Simulating projection ...

------------------------------------------------------------------------
Segmentation violation detected at Tue Dec 6 16:24:12 2016
------------------------------------------------------------------------

Configuration:
Crash Decoding : Disabled
Crash Mode : continue (default)
Current Graphics Driver: Unknown hardware
Current Visual : 0x21 (class 4, depth 24)
Default Encoding : UTF-8
GNU C Library : 2.21 stable
Host Name : localhost.localdomain
MATLAB Architecture : glnxa64
MATLAB Root : /usr/local/MATLAB/R2015b
MATLAB Version : 8.6.0.267246 (R2015b)
OpenGL : hardware
Operating System : Linux 4.0.4-301.fc22.x86_64 #1 SMP Thu May 21 13:10:33 UTC 2015 x86_64
Processor ID : x86 Family 6 Model 23 Stepping 10, GenuineIntel
Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : Fedora Project (11701000), display :0

Fault Count: 1

Abnormal termination:
Segmentation violation

Register State (from fault):
RAX = 0000000000000000 RBX = 0000000000000000
RCX = 0000000000000000 RDX = 00007f1706c41e60
RSP = 00007f175ccfbf80 RBP = 00007f16ed2dd5e0
RSI = 00007f1706c523f0 RDI = 0000000000000000

R8 = 00007f16d2ef8010 R9 = 0000000000000040
R10 = 0000000000000040 R11 = 0000000000000207
R12 = 0000000000000000 R13 = 00007f1706c41ba0
R14 = 00007f1706c523f0 R15 = 0000000000000000

RIP = 00007f16f1ca98eb EFL = 0000000000010202

CS = 0033 FS = 0000 GS = 0000

Stack Trace (from fault):
[ 0] 0x00007f16f1ca98eb /usr/local/niftyrec/lib/lib_et_line_integral_attenuated.so+00002283 _Z27et_line_integral_attenuatedP11nifti_imageS0_S0_if+00000027
[ 1] 0x00007f16f24b5253 /usr/local/niftyrec/lib/lib_et.so+00008787 _Z10et_projectP11nifti_imageS0_S0_S0_PfS1_iffi+00001411
[ 2] 0x00007f16f26bd3ca /usr/local/niftyrec/lib/lib_et_array_interface.so+00013258 SPECT_project_parallelholes+00001562
[ 3] 0x00007f16f28c825f /usr/local/niftyrec/niftyrec/matlab/et_project_mex.mexa64+00004703 mexFunction+00001327
[ 4] 0x00007f176633ec4a /usr/local/MATLAB/R2015b/bin/glnxa64/libmex.so+00142410 mexRunMexFile+00000090
[ 5] 0x00007f176633b244 /usr/local/MATLAB/R2015b/bin/glnxa64/libmex.so+00127556
[ 6] 0x00007f176633bde4 /usr/local/MATLAB/R2015b/bin/glnxa64/libmex.so+00130532
[ 7] 0x00007f176a8dfdbd /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_dispatcher.so+00724413 _ZN8Mfh_file16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00001549
[ 8] 0x00007f176a8e0250 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_dispatcher.so+00725584 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000032
[ 9] 0x00007f1764f588af /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+08612015
[ 10] 0x00007f176507c7ff /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+09807871
[ 11] 0x00007f1765072254 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+09765460
[ 12] 0x00007f176503f901 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+09558273
[ 13] 0x00007f1764ca1d6c /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+05766508
[ 14] 0x00007f1764c8c4c1 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+05678273
[ 15] 0x00007f1764c9b075 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+05738613
[ 16] 0x00007f1764e6c033 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07643187
[ 17] 0x00007f1764f4a3bc /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+08553404
[ 18] 0x00007f176a8dfb31 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_dispatcher.so+00723761 _ZN8Mfh_file16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000897
[ 19] 0x00007f176a8e0250 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_dispatcher.so+00725584 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000032
[ 20] 0x00007f1764f588af /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+08612015
[ 21] 0x00007f176507c7ff /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+09807871
[ 22] 0x00007f176507247f /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+09766015
[ 23] 0x00007f176503f981 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+09558401
[ 24] 0x00007f1764ca1d6c /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+05766508
[ 25] 0x00007f1764c8c4c1 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+05678273
[ 26] 0x00007f1764c9b075 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+05738613
[ 27] 0x00007f1764e6c033 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07643187
[ 28] 0x00007f1764e33c40 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07412800
[ 29] 0x00007f1764e36078 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07422072
[ 30] 0x00007f1764e36140 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07422272
[ 31] 0x00007f1764ead6bc /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07911100
[ 32] 0x00007f1764eadb42 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwm_lxe.so+07912258
[ 33] 0x00007f17665722bc /usr/local/MATLAB/R2015b/bin/glnxa64/libmwbridge.so+00168636
[ 34] 0x00007f1766572ef7 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwbridge.so+00171767 _Z8mnParserv+00000823
[ 35] 0x00007f176abc6b4f /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00686927 _ZN11mcrInstance30mnParser_on_interpreter_threadEv+00000031
[ 36] 0x00007f176abb3443 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00607299
[ 37] 0x00007f176abb3a39 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00608825 _ZN5boost6detail11task_objectIvNS_3_bi6bind_tIvPFvRKNS_8functionIFvvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025
[ 38] 0x00007f176abb4f47 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00614215 _ZN5boost6detail9task_baseIvE3runEv+00000071
[ 39] 0x00007f176abb4fa7 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00614311
[ 40] 0x00007f176abb02fa /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00594682
[ 41] 0x00007f175e76a6b6 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwuix.so+00313014
[ 42] 0x00007f175e75404a /usr/local/MATLAB/R2015b/bin/glnxa64/libmwuix.so+00221258
[ 43] 0x00007f175e7542bf /usr/local/MATLAB/R2015b/bin/glnxa64/libmwuix.so+00221887
[ 44] 0x00007f175e750987 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwuix.so+00207239
[ 45] 0x00007f176b547eae /usr/local/MATLAB/R2015b/bin/glnxa64/libmwservices.so+03010222
[ 46] 0x00007f176b54884c /usr/local/MATLAB/R2015b/bin/glnxa64/libmwservices.so+03012684 _Z25svWS_ProcessPendingEventsiib+00000092
[ 47] 0x00007f176abb09b8 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00596408
[ 48] 0x00007f176abb0cd4 /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00597204
[ 49] 0x00007f176ab9cfed /usr/local/MATLAB/R2015b/bin/glnxa64/libmwmcr.so+00516077
[ 50] 0x00007f1779ef9555 /lib64/libpthread.so.0+00030037
[ 51] 0x00007f1779c33ded /lib64/libc.so.6+01060333 clone+00000109
[ 52] 0x0000000000000000 <unknown-module>+00000000

This error was detected while a MEX-file was running. If the MEX-file
is not an official MathWorks function, please examine its source code
for errors. Please consult the External Interfaces Guide for information
on debugging MEX-files.

If this problem is reproducible, please submit a Service Request via:

http://www.mathworks.com/support/contact_us/

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /home/sn/matlab_crash_dump.3284-1 **

Caught MathWorks::System::FatalException
[Please exit and restart MATLAB]>>

Why do I get these errors? How can I solve it and run tt_... ?

Please guide me.
Thanks a lot.
Shahrokh

shahrokh
Newbie
Posts: 5
Permalink
Post Re: Some problems with running tt_demo_... ?!
on: December 14, 2016, 05:04
Quote

Hi,
I've stopped at this stage. I hope that you help me. I practice working with niftyrec in SPECT reconstruction in our nuclear medicine department. It is perfect to reconstruct SPECT from patients projections.
I want to use tt_... modules to reconstruct axial slices from EPID images acquired in our radiotherapy department.
Do not stop support for the project of niftyrec? Please reply to me.
I am looking forward to your guidance.
Shahrokh

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