[Mne_analysis] mne_epochs2mat error

Alexandre Gramfort gramfort at nmr.mgh.harvard.edu
Thu Jan 26 02:27:01 EST 2012
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another option is the mne-python module:

http://martinos.org/mne/auto_examples/plot_read_epochs.html

you can save a .mat file with python too.

Alex

On Wed, Jan 25, 2012 at 11:39 PM, Hari Bharadwaj
<hari at nmr.mgh.harvard.edu> wrote:
> Hi Conrad,
>    I haven't used mne_epochs2mat much.. I usually use
> mne_ex_read_epochs.m in the MATLAB toolbox.. It might be useful to use
> that instead to see if your downstream analysis is getting the same
> data as with mne_epochs2mat..
>
> Regards,
> Hari
>
>
>
> On Wed, January 25, 2012 4:15 pm, conrad at nmr.mgh.harvard.edu wrote:
>> Paul,
>>
>> While testing out the process on different machines and in different
>> environments I ran across a few new details that may help me figure out
>> what is happening.
>>
>> The machines I run the analysis on are martinos machines 'huygens' and
>> 'wittgenstein'. They are both linux computers(CentOS 5.7) and 64 bit. I
>> developed a GUI to encompass the analysis in Matlab, so whenever I run a
>> terminal command I just do "unix(____)" Sometimes I did not get the error
>> when running the command in terminal, but sometimes I still do. Generally,
>> Matlab or terminal, mne_epochs2mat does not like my machines.
>>
>> When I used the machine 'multnomah' (CentOS 4.7) to test the analysis it
>> was not happy with matlab7.11 (transcribed):
>>
>> [Warning: glibc 2.3.4 - Unsupported version.
>> [         glibc 2.7 - MATLAB built using this version
>> [
>> [Your configuration APPEARS to be too OLD to run this MATLAB program!
>>
>> So I ran it using matlab7.4 on multnomah. From these observations I
>> imagine it may have to deal with the glibc version used with the command
>> and the configuration of the computer. The program did not make any error
>> messages in this environment, however it's hard to read the error messages
>> since the program produces so much output so I could have missed it. It
>> seems that multnomah ran it fine, huygens and multnomah cannot.
>>
>> When I run it on matlab7.11 it start with this error message (but still
>> proceeds):
>>
>> [  I18N Runtime Warning:
>> [     Missing ICU data file detected while processing $(MATLAB)/bin/$(ARCH).
>> [     Hint: Check for a misconfigured environment or installation.
>> [
>> [  mne_epochs2mat.bin version 1.9 compiled at Jan 25 2012 04:22:57
>>
>> I was borrowing time on multnomah, it isn't actually my machine, so I
>> cannot run my analysis on it. Do you know a way to make it work on my
>> primary computers?
>>
>> Dan,
>>
>> The stable build produces the same error for me. I usually use the nightly
>> build though. However, what is matlab/octave?
>>
>> Thanks for your input!
>> - Conrad
>>
>>> You fail to state what machine you ran it on.  One likely issue it is
>>> too
>>> old either via its OS or its processor for running the programs.
>>>
>>> Have you run the exact same programs and data on another machine
>>> where it worked?  If so where?
>>>
>>> -- Paul Raines (http://help.nmr.mgh.harvard.edu)
>>>
>>>
>>>
>>> On Wed, 25 Jan 2012 3:13pm, conrad at nmr.mgh.harvard.edu wrote:
>>>
>>>> Hey MNE processors & help,
>>>>
>>>> I am still trying to figure out this error when I run mne_epochs2mat. I
>>>> originally had this problem in late October and no one identified the
>>>> problem. I'm still able to run my analysis but I'm not sure if it is
>>>> secretly corrupted or misaligned or something.
>>>>
>>>> Does anyone know where this error comes from and how it could affect
>>>> the
>>>> data?
>>>>
>>>> I can provide a more full explanation for the environment in which the
>>>> error occurs if that would help.
>>>>
>>>> - Conrad
>>>>
>>>> *** glibc detected ***
>>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin: double
>>>> free
>>>> or corruption (out): 0x000000000164c500 ***
>>>> ======= Backtrace: =========
>>>> /lib64/libc.so.6[0x33e6e7245f]
>>>> /lib64/libc.so.6(cfree+0x4b)[0x33e6e728bb]
>>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin(mne_free_name_list+0x5e)[0x41a60e]
>>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin(main+0x19f)[0x40bedf]
>>>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x33e6e1d994]
>>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin[0x40bbba]
>>>> ======= Memory map: ========
>>>> 00400000-004b3000 r-xp 00000000 00:1c 23226731
>>>> /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/mne/nightly_build/bin/mne_epochs2mat.bin
>>>> 005b2000-005b5000 rw-p 000b2000 00:1c 23226731
>>>> /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/mne/nightly_build/bin/mne_epochs2mat.bin
>>>> 005b5000-005c8000 rw-p 005b5000 00:00 0
>>>> 01585000-019a8000 rw-p 01585000 00:00 0
>>>> [heap]
>>>> 33e6a00000-33e6a1c000 r-xp 00000000 08:02 782032
>>>> /lib64/ld-2.5.so
>>>> 33e6c1c000-33e6c1d000 r--p 0001c000 08:02 782032
>>>> /lib64/ld-2.5.so
>>>> 33e6c1d000-33e6c1e000 rw-p 0001d000 08:02 782032
>>>> /lib64/ld-2.5.so
>>>> 33e6e00000-33e6f4e000 r-xp 00000000 08:02 782036
>>>> /lib64/libc-2.5.so
>>>> 33e6f4e000-33e714e000 ---p 0014e000 08:02 782036
>>>> /lib64/libc-2.5.so
>>>> 33e714e000-33e7152000 r--p 0014e000 08:02 782036
>>>> /lib64/libc-2.5.so
>>>> 33e7152000-33e7153000 rw-p 00152000 08:02 782036
>>>> /lib64/libc-2.5.so
>>>> 33e7153000-33e7158000 rw-p 33e7153000 00:00 0
>>>> 33e7200000-33e7282000 r-xp 00000000 08:02 782071
>>>> /lib64/libm-2.5.so
>>>> 33e7282000-33e7481000 ---p 00082000 08:02 782071
>>>> /lib64/libm-2.5.so
>>>> 33e7481000-33e7482000 r--p 00081000 08:02 782071
>>>> /lib64/libm-2.5.so
>>>> 33e7482000-33e7483000 rw-p 00082000 08:02 782071
>>>> /lib64/libm-2.5.so
>>>> 33e7600000-33e7602000 r-xp 00000000 08:02 782081
>>>> /lib64/libdl-2.5.so
>>>> 33e7602000-33e7802000 ---p 00002000 08:02 782081
>>>> /lib64/libdl-2.5.so
>>>> 33e7802000-33e7803000 r--p 00002000 08:02 782081
>>>> /lib64/libdl-2.5.so
>>>> 33e7803000-33e7804000 rw-p 00003000 08:02 782081
>>>> /lib64/libdl-2.5.so
>>>> 33e7a00000-33e7a16000 r-xp 00000000 08:02 782231
>>>> /lib64/libpthread-2.5.so
>>>> 33e7a16000-33e7c15000 ---p 00016000 08:02 782231
>>>> /lib64/libpthread-2.5.so
>>>> 33e7c15000-33e7c16000 r--p 00015000 08:02 782231
>>>> /lib64/libpthread-2.5.so
>>>> 33e7c16000-33e7c17000 rw-p 00016000 08:02 782231
>>>> /lib64/libpthread-2.5.so
>>>> 33e7c17000-33e7c1b000 rw-p 33e7c17000 00:00 0
>>>> 33eb600000-33eb607000 r-xp 00000000 08:02 782232
>>>> /lib64/librt-2.5.so
>>>> 33eb607000-33eb807000 ---p 00007000 08:02 782232
>>>> /lib64/librt-2.5.so
>>>> 33eb807000-33eb808000 r--p 00007000 08:02 782232
>>>> /lib64/librt-2.5.so
>>>> 33eb808000-33eb809000 rw-p 00008000 08:02 782232
>>>> /lib64/librt-2.5.so
>>>> 2b924bd5e000-2b924bd61000 rw-p 2b924bd5e000 00:00 0
>>>> 2b924bd8c000-2b924bd8d000 rw-p 2b924bd8c000 00:00 0
>>>> 2b924bd8d000-2b924bda6000 r-xp 00000000 00:1c 4787101
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmat.so
>>>> 2b924bda6000-2b924bea6000 ---p 00019000 00:1c 4787101
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmat.so
>>>> 2b924bea6000-2b924beab000 rw-p 00019000 00:1c 4787101
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmat.so
>>>> 2b924beab000-2b924bf01000 r-xp 00000000 00:1c 5841980
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmx.so
>>>> 2b924bf01000-2b924c000000 ---p 00056000 00:1c 5841980
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmx.so
>>>> 2b924c000000-2b924c00f000 rw-p 00055000 00:1c 5841980
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmx.so
>>>> 2b924c00f000-2b924c09f000 r-xp 00000000 00:1c 5842005
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libut.so
>>>> 2b924c09f000-2b924c19f000 ---p 00090000 00:1c 5842005
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libut.so
>>>> 2b924c19f000-2b924c1c2000 rw-p 00090000 00:1c 5842005
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libut.so
>>>> 2b924c1c2000-2b924c4d8000 rw-p 2b924c1c2000 00:00 0
>>>> 2b924c4d8000-2b924c56e000 r-xp 00000000 08:02 1736152
>>>> /usr/lib64/libgfortran.so.1.0.0
>>>> 2b924c56e000-2b924c76d000 ---p 00096000 08:02 1736152
>>>> /usr/lib64/libgfortran.so.1.0.0
>>>> 2b924c76d000-2b924c76f000 rw-p 00095000 08:02 1736152
>>>> /usr/lib64/libgfortran.so.1.0.0
>>>> 2b924c76f000-2b924c770000 rw-p 2b924c76f000 00:00 0
>>>> 2b924c770000-2b924c87d000 r-xp 00000000 00:1c 4787093
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libhdf5.so.0.0.0
>>>> 2b924c87d000-2b924c97c000 ---p 0010d000 00:1c 4787093
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libhdf5.so.0.0.0
>>>> 2b924c97c000-2b924c98e000 rw-p 0010c000 00:1c 4787093
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libhdf5.so.0.0.0
>>>> 2b924c98e000-2b924c98f000 rw-p 2b924c98e000 00:00 0
>>>> 2b924c98f000-2b924ca5c000 r-xp 00000000 00:1c 4542391
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libstdc++.so.6.0.8
>>>> 2b924ca5c000-2b924cb5c000 ---p 000cd000 00:1c 4542391
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libstdc++.so.6.0.8
>>>> 2b924cb5c000-2b924cb7d000 rw-p 000cd000 00:1c 4542391
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libstdc++.so.6.0.8
>>>> 2b924cb7d000-2b924cb90000 rw-p 2b924cb7d000 00:00 0
>>>> 2b924cb90000-2b924cb9c000 r-xp 00000000 00:1c 4542388
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1
>>>> 2b924cb9c000-2b924cc9b000 ---p 0000c000 00:1c 4542388
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1
>>>> 2b924cc9b000-2b924cc9d000 rw-p 0000b000 00:1c 4542388
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1
>>>> 2b924cc9d000-2b924cc9e000 rw-p 2b924cc9d000 00:00 0
>>>> 2b924cc9e000-2b924cc9f000 r-xp 00000000 00:1c 4787095
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicudata.so.32.0
>>>> 2b924cc9f000-2b924cd9e000 ---p 00001000 00:1c 4787095
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicudata.so.32.0
>>>> 2b924cd9e000-2b924cd9f000 rw-p 00000000 00:1c 4787095
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicudata.so.32.0
>>>> 2b924cd9f000-2b924ce7f000 r-xp 00000000 00:1c 4787098
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuuc.so.32.0
>>>> 2b924ce7f000-2b924cf7e000 ---p 000e0000 00:1c 4787098
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuuc.so.32.0
>>>> 2b924cf7e000-2b924cf8b000 rw-p 000df000 00:1c 4787098
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuuc.so.32.0
>>>> 2b924cf8b000-2b924cf8d000 rw-p 2b924cf8b000 00:00 0
>>>> 2b924cf8d000-2b924d0ae000 r-xp 00000000 00:1c 4787096
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicui18n.so.32.0
>>>> 2b924d0ae000-2b924d1ad000 ---p 00121000 00:1c 4787096
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicui18n.so.32.0
>>>> 2b924d1ad000-2b924d1b6000 rw-p 00120000 00:1c 4787096
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicui18n.so.32.0
>>>> 2b924d1b6000-2b924d1c0000 r-xp 00000000 00:1c 4787097
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuio.so.32.0
>>>> 2b924d1c0000-2b924d2c0000 ---p 0000a000 00:1c 4787097
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuio.so.32.0
>>>> 2b924d2c0000-2b924d2c2000 rw-p 0000a000 00:1c 4787097
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuio.so.32.0
>>>> 2b924d2c2000-2b924d2ce000 r-xp 00000000 00:1c 5842011
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libz.so.1.1.4
>>>> 2b924d2ce000-2b924d3ce000 ---p 0000c000 00:1c 5842011
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libz.so.1.1.4
>>>> 2b924d3ce000-2b924d3d1000 rw-p 0000c000 00:1c 5842011
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libz.so.1.1.4
>>>> 2b924d3d1000-2b924d3d5000 rw-p 2b924d3d1000 00:00 0
>>>> 2b924d3d5000-2b924dd27000 r--s 00000000 00:1c 4787071
>>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/icudt32l.dat
>>>> 2b924dd27000-2b924de68000 rw-p 2b924dd27000 00:00 0
>>>> 2b927275e000-2b9275d2b000 r--p 00000000 08:02 1748532
>>>> /usr/lib/locale/locale-archive
>>>> 7fff81478000-7fff8148c000 rwxp 7ffffffe8000 00:00 0
>>>> [stack]
>>>> 7fff8148c000-7fff8148e000 rw-p 7fffffffd000 00:00 0
>>>> 7fff8153d000-7fff81540000 r-xp 7fff8153d000 00:00 0
>>>> [vdso]
>>>> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
>>>> [vsyscall]
>>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat: line 68:
>>>> 15797
>>>> Aborted
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
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>>
>>
>>
>
>
> --
> Hari Bharadwaj
> _______________________________________________
> Mne_analysis mailing list
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>
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