[MINC-users] minctracc glibc error detected

[Mishkin Derakhshan]

Sorry, I had to redact some information from the filenames for privacy
reasons. But none of the filenames were over 256 chars.

The actual filenames were like this:
Source has 61 chars
target has 55
model_mask has 66
transformation has 69
measure has 67



On Tue, Jul 12, 2016 at 7:17 PM, Vladimir S. Fonov <vladimir.fonov at gmail.com
> wrote:

> No, that's not it - the example doesn't have long file names.
>
>
> On 16-07-12 10:22 PM, Robert D. Vincent wrote:
>
>> Hi,
>>
>> I can't be certain, but looking through the git history I see at least one
>> possibility:
>>
>> https://github.com/BIC-MNI/mni_autoreg/issues/7
>>
>>      -bert
>>
>>
>> On Tue, Jul 12, 2016 at 4:23 PM, Mishkin Derakhshan <mishkind at gmail.com>
>> wrote:
>>
>> Aloha,
>>>
>>> For reasons I won't get into here, I am using an older version of
>>> minctracc
>>>
>>> mni-autoreg version 0.99.2
>>> $ minctracc -version
>>> The program <minctracc> was built from:
>>> Package mni_autoreg 0.99.2, compiled by rotor at romeo (i686-pc-linux-gnu)
>>> on
>>> Mon May  8 23:16:34 EDT 2006
>>>
>>> minc version 1.4
>>> $ mincinfo -version
>>> program: 1.4
>>> libminc: 1.4
>>> netcdf : 3.6.1 of May 11 2015 21:32:07 $
>>>
>>>
>>> The problem is that *sometimes* I get core dumps, i.e., on some subjects
>>> but not all. From what I can google from the error, I'm guessing it is an
>>> array out of bounds issue, and I'm also going to guess this was fixed in
>>> a
>>> later release of mni-autoreg or minc. Can anyone point me in the right
>>> direction. I'm hoping that maybe I can apply a small patch to minctracc
>>> in
>>> 0.99.2, recompile it, and then still have a version of minctracc that
>>> produces the same results as 0.99.2 in the cases where it doesn't fail.
>>>
>>> Mahalo,
>>> mishkin
>>>
>>> Here is a sample command line:
>>> minctracc stx_brain.mnc.gz stx.mnc.gz -model_mask stx_brain_mask.mnc.gz
>>> -transformation stx_analyze2minc_res.xfm -measure stx_brain_xfm_eval.txt
>>> -clobber
>>>
>>> Here is the default error/output:
>>> *** glibc detected *** free(): invalid next size (normal): 0x080e0808 ***
>>>
>>> Here is the debugging output:
>>> *** glibc detected *** minctracc: free(): invalid next size (normal):
>>> 0x08e9e560 ***
>>> ======= Backtrace: =========
>>> /lib/libc.so.6(+0x70c91)[0x55657c91]
>>> /lib/libc.so.6(+0x736f1)[0x5565a6f1]
>>> minctracc[0x80a3ea8]
>>> minctracc[0x80501af]
>>> minctracc[0x8051461]
>>> minctracc[0x8053e8c]
>>> minctracc[0x804c06a]
>>> /lib/libc.so.6(__libc_start_main+0xe6)[0x555fdd26]
>>> minctracc[0x8049881]
>>> ======= Memory map: ========
>>> 08048000-080d5000 r-xp 00000000 00:13 52030078
>>> minctracc
>>> 080d5000-080d8000 rw-p 0008d000 00:13 52030078
>>>   minctracc
>>> 080d8000-080da000 rw-p 00000000 00:00 0
>>> 08e96000-08eee000 rw-p 00000000 00:00 0
>>>   [heap]
>>> 55555000-55573000 r-xp 00000000 fd:01 18326
>>>   /lib/ld-2.12.so
>>> 55573000-55574000 r--p 0001e000 fd:01 18326
>>>   /lib/ld-2.12.so
>>> 55574000-55575000 rw-p 0001f000 fd:01 18326
>>>   /lib/ld-2.12.so
>>> 55575000-55576000 r-xp 00000000 00:00 0
>>>   [vdso]
>>> 55576000-55577000 rw-p 00000000 00:00 0
>>> 55577000-555ab000 r-xp 00000000 00:13 51884124
>>> libnetcdf.so.3.6.1
>>> 555ab000-555ac000 rw-p 00034000 00:13 51884124
>>> libnetcdf.so.3.6.1
>>> 555ac000-555af000 rw-p 00000000 00:00 0
>>> 555bd000-555e5000 r-xp 00000000 fd:01 15234
>>>   /lib/libm-2.12.so
>>> 555e5000-555e6000 r--p 00027000 fd:01 15234
>>>   /lib/libm-2.12.so
>>> 555e6000-555e7000 rw-p 00028000 fd:01 15234
>>>   /lib/libm-2.12.so
>>> 555e7000-55778000 r-xp 00000000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 55778000-55779000 ---p 00191000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 55779000-5577b000 r--p 00191000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 5577b000-5577c000 rw-p 00193000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 5577c000-56e45000 rw-p 00000000 00:00 0
>>> 56e55000-56e72000 r-xp 00000000 fd:01 12959
>>>   /lib/libgcc_s-4.4.7-20120601.so.1
>>> 56e72000-56e73000 rw-p 0001d000 fd:01 12959
>>>   /lib/libgcc_s-4.4.7-20120601.so.1
>>> 56f00000-56f21000 rw-p 00000000 00:00 0
>>> 56f21000-57000000 ---p 00000000 00:00 0
>>> ffbfd000-ffc13000 rw-p 00000000 00:00 0
>>>   [stack]
>>> Abort (core dumped)
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
> _______________________________________________
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> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>