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vvs4
Junior Member
USA
40 Posts |
 Posted - Jan 18 2011 : 09:03:35 AM
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Hi BIAC!
I am working on fitting some p-files with bxh headers for conversion to other file types. When I try to use pfile2bxh or bxhabsorb I get the following error:
[vvs4@node58 faces]$ bxhabsorb --fromtype pfile P28194.7 output.bxh
Warning: I don't recognize PSD epimecho -- some values may be incorrect.
Warning: reported slice spacing (3.3) is different from calculated spacing (0.464625) by more than 0.005. Using calculated number.
*** glibc detected *** pfile2bxh: double free or corruption (out): 0x0000000003d8a4f0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x2b75fe4b430f]
/lib64/libc.so.6(cfree+0x4b)[0x2b75fe4b476b]
pfile2bxh[0x4293d8]
pfile2bxh[0x40848e]
pfile2bxh[0x40747c]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x2b75fe45f994]
pfile2bxh[0x40695a]
======= Memory map: ========
00400000-006ce000 r-xp 00000000 00:13 162312583 /usr/local/packages/bxh_xcede_tools-1.9.8.9/bin/bxhabsorb
007ce000-007ff000 rwxp 002ce000 00:13 162312583 /usr/local/packages/bxh_xcede_tools-1.9.8.9/bin/bxhabsorb
007ff000-00808000 rwxp 007ff000 00:00 0
03cc6000-03dae000 rwxp 03cc6000 00:00 0 [heap]
3136000000-3136014000 r-xp 00000000 00:13 1497861017 /usr/lib64/libz.so.1.2.3
3136014000-3136213000 ---p 00014000 00:13 1497861017 /usr/lib64/libz.so.1.2.3
3136213000-3136214000 rwxp 00013000 00:13 1497861017 /usr/lib64/libz.so.1.2.3
2b75fd878000-2b75fd894000 r-xp 00000000 00:13 662024820 /lib64/ld-2.5.so
2b75fd894000-2b75fd899000 rwxp 2b75fd894000 00:00 0
2b75fd8b3000-2b75fd8b4000 rwxp 2b75fd8b3000 00:00 0
2b75fda93000-2b75fda94000 r-xp 0001b000 00:13 662024820 /lib64/ld-2.5.so
2b75fda94000-2b75fda95000 rwxp 0001c000 00:13 662024820 /lib64/ld-2.5.so
2b75fda95000-2b75fdb17000 r-xp 00000000 00:13 142257483 /lib64/libm-2.5.so
2b75fdb17000-2b75fdd16000 ---p 00082000 00:13 142257483 /lib64/libm-2.5.so
2b75fdd16000-2b75fdd17000 r-xp 00081000 00:13 142257483 /lib64/libm-2.5.so
2b75fdd17000-2b75fdd18000 rwxp 00082000 00:13 142257483 /lib64/libm-2.5.so
2b75fdd18000-2b75fdd2e000 r-xp 00000000 00:13 2311272166 /lib64/libpthread-2.5.so
2b75fdd2e000-2b75fdf2d000 ---p 00016000 00:13 2311272166 /lib64/libpthread-2.5.so
2b75fdf2d000-2b75fdf2e000 r-xp 00015000 00:13 2311272166 /lib64/libpthread-2.5.so
2b75fdf2e000-2b75fdf2f000 rwxp 00016000 00:13 2311272166 /lib64/libpthread-2.5.so
2b75fdf2f000-2b75fdf34000 rwxp 2b75fdf2f000 00:00 0
2b75fdf34000-2b75fe01a000 r-xp 00000000 00:13 3513790799 /usr/lib64/libstdc++.so.6.0.8
2b75fe01a000-2b75fe219000 ---p 000e6000 00:13 3513790799 /usr/lib64/libstdc++.so.6.0.8
2b75fe219000-2b75fe21f000 r-xp 000e5000 00:13 3513790799 /usr/lib64/libstdc++.so.6.0.8
2b75fe21f000-2b75fe222000 rwxp 000eb000 00:13 3513790799 /usr/lib64/libstdc++.so.6.0.8
2b75fe222000-2b75fe234000 rwxp 2b75fe222000 00:00 0
2b75fe234000-2b75fe241000 r-xp 00000000 00:13 3569367290 /lib64/libgcc_s-4.1.2-20080825.so.1
2b75fe241000-2b75fe441000 ---p 0000d000 00:13 3569367290 /lib64/libgcc_s-4.1.2-20080825.so.1
2b75fe441000-2b75fe442000 rwxp 0000d000 00:13 3569367290 /lib64/libgcc_s-4.1.2-20080825.so.1
2b75fe442000-2b75fe590000 r-xp 00000000 00:13 2781118436 /lib64/libc-2.5.so
2b75fe590000-2b75fe78f000 ---p 0014e000 00:13 2781118436 /lib64/libc-2.5.so
2b75fe78f000-2b75fe793000 r-xp 0014d000 00:13 2781118436 /lib64/libc-2.5.so
2b75fe793000-2b75fe794000 rwxp 00151000 00:13 2781118436 /lib64/libc-2.5.so
2b75fe794000-2b75fe79b000 rwxp 2b75fe794000 00:00 0
7fff463a3000-7fff463b9000 rw-p 7ffffffe8000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
Aborted
Whenever I see the work "corruption" it gives me the heebie jeebies - and since I know that these files are older and I haven't seen a lot of posts about errors with pfiles and the bxh tools, I am guessing that it is something about my file. I am currently installing xv and rdgehdr (http://rsl.stanford.edu/research/software.html) to see if I can poke in to get any information about the files. If anyone has any suggestions it would be greatly appreciated - I will post any significant updates!
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-Vanessa |
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vvs4
Junior Member
USA
40 Posts |
Posted - Jan 18 2011 : 09:28:21 AM
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Here is the p-file information that I extracted. I am still looking through it myself, but I wanted to put it up asap!
http://www.vsoch.com/LONG/Send/pfile.txt |
-Vanessa |
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petty
BIAC Staff
USA
453 Posts |
Posted - Jan 18 2011 : 09:29:37 AM
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hey vanessa, i don't see where you've included the images that you are trying to create the BXH header for..
you should be running: pfile2bxh P28194.7 *.img output.bxh |
Edited by - petty on Jan 18 2011 09:30:20 AM |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jan 18 2011 : 09:47:51 AM
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Hey Vanessa,
The memory corruption is definitely something I need to fix, but it is probably related to something more fundamental, and may have something to do with this being a sequence that we haven't tested with before. Each sequence may have some key fields stored in different places. I'd have to look at the actual Pfile header to be sure. If you could just extract the header like this (should work on the interactive node):
dd if=P28194.7 bs=200K count=1 | gzip -c - > tmp.pfh.gz
and send me tmp.pfh.gz by email.
Also, as Chris says, you will need reconstructed images too; our convention is to name them *.img but could be different for your data. If you don't have reconstructed images, and just have the Pfile, then you probably need to find a reconstruction program for this particular pulse sequence to extract the image data out of the Pfile. |
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P-file Conversion Error
