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Bug 1068 - ft_read_mri causing a system error
| Status | CLOSED WORKSFORME |
| Reported | 2011-10-24 11:57:00 +0200 |
| Modified | 2011-11-09 16:44:53 +0100 |
| Product: | FieldTrip |
| Component: | fileio |
| Version: | unspecified |
| Hardware: | Other |
| Operating System: | Linux |
| Importance: | P1 major |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Lilla Magyari - 2011-10-24 11:57:39 +0200
Hi, I have downloaded the 20111021 (latest) version of FT (because I am using it at the MPI), and when I try to use ft_read_mri (reading .nii or .ima images), I get a system error. This worked with earlier version of FT. I have attached one of the anatomical data that I can not read in anymore. Lilla mri = ft_read_mri('nse20080604.nii'); This is the error: ------------------------------------------------------------------------ Floating point exception detected at Mon Oct 24 11:30:43 2011 ------------------------------------------------------------------------ Configuration: MATLAB Version: 7.7.0.471 (R2008b) MATLAB License: 38957 Operating System: Linux 2.6.16.46-0.12-smp #1 SMP Thu May 17 14:00:09 UTC 2007 x86_64 GNU C Library: 2.4 development Window System: The XFree86 Project, Inc (40201000), display lux20.mpi.nl:21.0 Current Visual: 0x22 (class 4, depth 16) Processor ID: x86 Family 6 Model 15 Stepping 7, GenuineIntel Virtual Machine: Java 1.6.0_04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode Default Encoding: US-ASCII Fault Count: 1 Register State: rax = 000000000f4d007f rbx = 0000000000000000 rcx = 00000000407cad60 rdx = 0000000000000000 rbp = 00000000407cada0 rsi = 000000000f4d007f rdi = 00002aaac9d003e1 rsp = 00000000407cabf0 r8 = 000000000252b1d0 r9 = 0000000000000000 r10 = 0000000000000000 r11 = 0000000000000000 r12 = 00000000407cad60 r13 = 000000000252af20 r14 = 0000000000000000 r15 = 00002aaac9d00188 rip = 00002b0d5f56168f flg = 0000000000010246 Stack Trace: [0] ld-linux-x86-64.so.2:0x00002b0d5f56168f(1, 0, 0x2aaac9d001b8, 0x0252af20) [1] ld-linux-x86-64.so.2:0x00002b0d5f563028(0, 0xffffffff80000002, 0x407cb040, 0x2b0d80000002) [2] ld-linux-x86-64.so.2:0x00002b0d5f5692a5(0x407cb040, 0x2b0d5f568ed0, 0x407cb09f, 0x407cb088) [3] ld-linux-x86-64.so.2:0x00002b0d5f5651f6(0x0068a780, 0, 0, 0x407cb260) [4] libdl.so.2:0x00002b0d616c31fa(40, 0x2b0d5f6b3c11, 0x014e93e0, 0x2b0d5f6b3c11) 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 it is an official MathWorks function, please follow these steps to report this problem to The MathWorks so we have the best chance of correcting it: The next time MATLAB is launched under typical usage, a dialog box will open to help you send the error log to The MathWorks. Alternatively, you can send an e-mail to segv@mathworks.com with the following file attached: /home/lilmag/matlab_crash_dump.10350 If the problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ts/help_request_1.html A technical support engineer might contact you with further information. Thank you for your help. MATLAB may attempt to recover, but even if recovery appears successful, we recommend that you save your workspace and restart MATLAB as soon as possible. ------------------------------------------------------------------------ Segmentation violation detected at Mon Oct 24 11:52:05 2011 ------------------------------------------------------------------------ Configuration: MATLAB Version: 7.7.0.471 (R2008b) MATLAB License: 38957 Operating System: Linux 2.6.16.46-0.12-smp #1 SMP Thu May 17 14:00:09 UTC 2007 x86_64 GNU C Library: 2.4 development Window System: The XFree86 Project, Inc (40201000), display lux20.mpi.nl:21.0 Current Visual: 0x22 (class 4, depth 16) Processor ID: x86 Family 6 Model 15 Stepping 7, GenuineIntel Virtual Machine: Java 1.6.0_04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode Default Encoding: US-ASCII Fault Count: 2 Register State: rax = 0000001f00000001 rbx = 00002b0d5f855274 rcx = 00000000407cfdf8 rdx = 00000000006dff60 rbp = 00000000407cfec0 rsi = 00000000407cfe00 rdi = 00000000407cfc40 rsp = 00000000407cfe00 r8 = 0000000000000007 r9 = 00002b0d60311a08 r10 = 00002b0d602f7000 r11 = 00002b0d6126f4c0 r12 = 0000000001fe5650 r13 = 0000000000000007 r14 = 0000000000591d20 r15 = 00000000407d0020 rip = 00002b0d6030c25b flg = 0000000000010202 Stack Trace: [0] libmwbridge.so:mnParser(0x00596e80, 0x00596e10, 0x00591d40, 0x00591d20) + 1595 bytes [1] libmwmcr.so:mcrInstance::mnParser()(0x407d014f, 0x407d0140 "?-Y", 0x7fff4b54f558, 0x100000000) + 82 bytes [2] MATLAB:mcrMain(int, char const**)(0x407d01d0, 0x407d0940, 0, 0x2b0d612760b0) + 493 bytes [3] libmwmcr.so:runMcrMain(void*)(0, 0x407d0940, 0x407d0940, 0xff8c0aa3aea35ebb) + 28 bytes Segmentation violation occurred within signal handler. Unable to complete stack trace (stack was probably corrupted) Please follow these steps to report this problem to The MathWorks so we have the best chance of correcting it: The next time MATLAB is launched under typical usage, a dialog box will open to help you send the error log to The MathWorks. Alternatively, you can send an e-mail to segv@mathworks.com with the following file attached: /home/lilmag/matlab_crash_dump.10350 If the problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ts/help_request_1.html A technical support engineer might contact you with further information. Thank you for your help.
Lilla Magyari - 2011-10-24 11:58:41 +0200
of course, I could not attach the anatomical data.
Jan-Mathijs Schoffelen - 2011-11-02 14:35:12 +0100
Is it solved? For me it just works... (I took the 'nse20080604.nii' from your home directory
Cristiano Micheli - 2011-11-02 19:31:22 +0100
Hi Jan-Mathijs Apparently I have the same problem reading the anatomical MRI (I could read it yesterday, what happened in between?) -ON execution of the following code:- anat = '~/Pele/results/forward/MRI/monkeySPM_MRI/pele20060428/orig/pele20060428.nii'; ana = ft_read_mri(anat); -I get the following message- ??? Error using ==> spm_slice_vol Cant open image file. Error in ==> spm_read_vols at 34 Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 p]),V(i).dim(1:2),0); Error in ==> ft_read_mri at 93 img = spm_read_vols(hdr); Any idea? C