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CoBrALab / quarantine

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CIVET file name length #13

Open raihaan opened 9 years ago

raihaan commented 9 years ago

for filenames > 250 characters, CIVET throws an error

mincblur-clobber-fwhm4/data/chamal/projects/raihaan/civet-course/3T/civet2/output/ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789/classify/testrun_ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789_artefact.mnc_temp/data/chamal/projects/raihaan/civet-course/3T/civet2/output/ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789/classify/testrun_ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789_artefact.mnc* stack smashing detected *: mincblur terminated ======= Backtrace: ========= /lib/libc.so.6(fortify_fail+0x37)[0x2b0d4a0d1287] /lib/libc.so.6(__fortify_fail+0x0)[0x2b0d4a0d1250] mincblur[0x40e4fa] mincblur[0x412a13] /lib/libc.so.6(libc_start_main+0xfd)[0x2b0d4a00bc8d] mincblur[0x40a469] ======= Memory map: ======== 00400000-00564000 r-xp 00000000 00:1e 102382306 /opt/quarantine/CIVET/1.1.10/build/bin/mincblur 00764000-0076a000 rw-p 00164000 00:1e 102382306 /opt/quarantine/CIVET/1.1.10/build/bin/mincblur 0076a000-0076d000 rw-p 00000000 00:00 0 00941000-00da8000 rw-p 00000000 00:00 0 [heap] 2b0d49934000-2b0d49952000 r-xp 00000000 08:01 33516 /lib/ld-2.11.3.so 2b0d49952000-2b0d49954000 rw-p 00000000 00:00 0 2b0d49969000-2b0d49a6b000 rw-p 00000000 00:00 0 2b0d49b51000-2b0d49b52000 r--p 0001d000 08:01 33516 /lib/ld-2.11.3.so 2b0d49b52000-2b0d49b53000 rw-p 0001e000 08:01 33516 /lib/ld-2.11.3.so 2b0d49b53000-2b0d49b54000 rw-p 00000000 00:00 0 2b0d49b54000-2b0d49bd4000 r-xp 00000000 08:01 33541 /lib/libm-2.11.3.so 2b0d49bd4000-2b0d49dd4000 ---p 00080000 08:01 33541 /lib/libm-2.11.3.so 2b0d49dd4000-2b0d49dd5000 r--p 00080000 08:01 33541 /lib/libm-2.11.3.so 2b0d49dd5000-2b0d49dd6000 rw-p 00081000 08:01 33541 /lib/libm-2.11.3.so 2b0d49dd6000-2b0d49ded000 r-xp 00000000 08:0a 691223 /usr/lib/libz.so.1.2.3.4 2b0d49ded000-2b0d49fec000 ---p 00017000 08:0a 691223 /usr/lib/libz.so.1.2.3.4 2b0d49fec000-2b0d49fed000 rw-p 00016000 08:0a 691223 /usr/lib/libz.so.1.2.3.4 2b0d49fed000-2b0d4a146000 r-xp 00000000 08:01 33523 /lib/libc-2.11.3.so 2b0d4a146000-2b0d4a345000 ---p 00159000 08:01 33523 /lib/libc-2.11.3.so 2b0d4a345000-2b0d4a349000 r--p 00158000 08:01 33523 /lib/libc-2.11.3.so 2b0d4a349000-2b0d4a34a000 rw-p 0015c000 08:01 33523 /lib/libc-2.11.3.so 2b0d4a34a000-2b0d4be6e000 rw-p 00000000 00:00 0 2b0d4be6e000-2b0d4be84000 r-xp 00000000 08:01 31554 /lib/libgcc_s.so.1 2b0d4be84000-2b0d4c083000 ---p 00016000 08:01 31554 /lib/libgcc_s.so.1 2b0d4c083000-2b0d4c084000 rw-p 00015000 08:01 31554 /lib/libgcc_s.so.1 7fff8a228000-7fff8a25b000 rw-p 00000000 00:00 0 [stack] 7fff8a3ff000-7fff8a400000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Making byte volume... system mincblur -clobber -fwhm 4 /data/chamal/projects/raihaan/civet-course/3T/civet2/output/ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789/classify/testrun_ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789_artefact.mnc_temp /data/chamal/projects/raihaan/civet-course/3T/civet2/output/ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789/classify/testrun_ADNI_005_S_0553_MR_MPRGradWarpB1_CorrectionN3Scaled_Br_20081014174211298_S53157_I120789_artefact.mnc failed: 134 at /opt/quarantine/CIVET/1.1.10/build/CIVET-1.1.10/progs/class_art line 35.

gdevenyi commented 9 years ago

Core dump indicates a bug in blur_volume.c mni_autoreg/mincblur

gdevenyi commented 9 years ago

Haha! Success!

  char
    full_outfilename[256];      /* name of output file */
raihaan commented 9 years ago

nice find

On Wed, Oct 1, 2014 at 6:17 PM, Gabriel A. Devenyi <notifications@github.com

wrote:

Haha! Success!

char full_outfilename[256]; /* name of output file */

— Reply to this email directly or view it on GitHub https://github.com/CobraLab/quarantine/issues/13#issuecomment-57550046.

gdevenyi commented 9 years ago

Finding filename buffer declarations

find . -name '*.c' -type f -exec grep -E -n -i -H '.*file.*\[[0-9]{2,}\]' {} \;
gdevenyi commented 9 years ago

Bugs also exist in CIVET/1.1.12:

./mni_autoreg-0.99.6/mincblur/gradient_volume.c:    full_outfilename[256];        /* name of output file */
./mni_autoreg-0.99.6/mincblur/mincblur.c:    reals_filename[1024];
./mni_autoreg-0.99.6/mincblur/blur_volume.c:    full_outfilename[256];        /* name of output file */
./pve-1.3.0/pve.c:  char outfilename[255]; 
./pve-1.3.0/pve.c:  char tag_filename[255];
./pve-1.3.0/pve3.c:  char outfilename[255]; 
./pve-1.3.0/pve3.c:  char tag_filename[255];
gdevenyi commented 9 years ago

Better search, returns values between 0 and 1023

> find . -type f \( -name '*.c' -o -name '*.h' \)  -exec grep -E -n -i -H '.*file.*\[0*([1-9][0-9]{1,2}|10[01][0-9]|102[0-3])\]' {} \;

Regex from http://utilitymill.com/utility/Regex_For_Range