Scinet: minc-toolkit v.s. minc-tools/mice-chihiro

[raihaan]

While searching for answers on a dataset that I have been having trouble running through MAGeT, noticed that data in these files is unsigned short, while atlases as well as my previous successful MAGeT runs were signed short. Thought it worth a shot to resample to signed shorts and test with MAGeT.

with minc-tookit/1.0.01 loaded:  mincresample -signed $file $file -clobber
ran for some files but not for all...
Transforming slices:................................................................................................................................................................................Done
*** glibc detected *** mincresample: double free or corruption (!prev): 0x00000000011b8bc0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x760e6)[0x7fd46befd0e6]
/lib64/libc.so.6(+0x78c13)[0x7fd46beffc13]
/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/lib/libminc2.so.3.0.0(H5FL_garbage_coll+0x11f)[0x7fd46c7e9d3f]
/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/lib/libminc2.so.3.0.0(H5FL_term_interface+0x9)[0x7fd46c7eb039]
/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/lib/libminc2.so.3.0.0(+0xe45f5)[0x7fd46c7865f5]
/lib64/libc.so.6(exit+0xe2)[0x7fd46bebcda2]
mincresample[0x4025a7]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x7fd46bea5cdd]
mincresample[0x402459]
======= Memory map: ========
00400000-00411000 r-xp 00000000 00:15 128847612                          /scratch/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/bin/mincresample
00610000-00612000 rw-p 00010000 00:15 128847612                          /scratch/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/bin/mincresample
01178000-01329000 rw-p 00000000 00:00 0                                  [heap]
7fd46a16c000-7fd46b686000 rw-p 00000000 00:00 0
7fd46bc72000-7fd46bc87000 r-xp 00000000 00:16 69056998                   /home/scinet/gpc/compilers/gcc-4.6.1/lib64/libgcc_s.so.1
7fd46bc87000-7fd46be86000 ---p 00015000 00:16 69056998                   /home/scinet/gpc/compilers/gcc-4.6.1/lib64/libgcc_s.so.1
7fd46be86000-7fd46be87000 rw-p 00014000 00:16 69056998                   /home/scinet/gpc/compilers/gcc-4.6.1/lib64/libgcc_s.so.1
7fd46be87000-7fd46c011000 r-xp 00000000 00:10 126471                     /lib64/libc-2.12.so
7fd46c011000-7fd46c210000 ---p 0018a000 00:10 126471                     /lib64/libc-2.12.so
7fd46c210000-7fd46c214000 r--p 00189000 00:10 126471                     /lib64/libc-2.12.so
7fd46c214000-7fd46c215000 rw-p 0018d000 00:10 126471                     /lib64/libc-2.12.so
7fd46c215000-7fd46c21a000 rw-p 00000000 00:00 0
7fd46c21a000-7fd46c21c000 r-xp 00000000 00:10 126556                     /lib64/libdl-2.12.so
7fd46c21c000-7fd46c41c000 ---p 00002000 00:10 126556                     /lib64/libdl-2.12.so
7fd46c41c000-7fd46c41d000 r--p 00002000 00:10 126556                     /lib64/libdl-2.12.so
7fd46c41d000-7fd46c41e000 rw-p 00003000 00:10 126556                     /lib64/libdl-2.12.so
7fd46c41e000-7fd46c4a1000 r-xp 00000000 00:10 126711                     /lib64/libm-2.12.so
7fd46c4a1000-7fd46c6a0000 ---p 00083000 00:10 126711                     /lib64/libm-2.12.so
7fd46c6a0000-7fd46c6a1000 r--p 00082000 00:10 126711                     /lib64/libm-2.12.so
7fd46c6a1000-7fd46c6a2000 rw-p 00083000 00:10 126711                     /lib64/libm-2.12.so
7fd46c6a2000-7fd46ca72000 r-xp 00000000 00:15 137040019                  /scratch/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/lib/libminc2.so.2.3.00
7fd46ca72000-7fd46cc71000 ---p 003d0000 00:15 137040019                  /scratch/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/lib/libminc2.so.2.3.00
7fd46cc71000-7fd46cccd000 rw-p 003cf000 00:15 137040019                  /scratch/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/lib/libminc2.so.2.3.00
7fd46cccd000-7fd46ccd5000 rw-p 00000000 00:00 0
7fd46ccd5000-7fd46ccf5000 r-xp 00000000 00:10 126579                     /lib64/ld-2.12.so
7fd46cede000-7fd46cee1000 rw-p 00000000 00:00 0
7fd46cef1000-7fd46cef4000 rw-p 00000000 00:00 0
7fd46cef4000-7fd46cef5000 r--p 0001f000 00:10 126579                     /lib64/ld-2.12.so
7fd46cef5000-7fd46cef6000 rw-p 00020000 00:10 126579                     /lib64/ld-2.12.so
7fd46cef6000-7fd46cef7000 rw-p 00000000 00:00 0
7fff5526c000-7fff5529b000 rw-p 00000000 00:00 0                          [stack]
7fff553b3000-7fff553b4000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted
Transforming slices:................................................................................................................................................................................Done
Transforming slices:................................................................................................................................................................................Done
Segmentation fault
Transforming slices:................................................................................................................................................................................Done

unloaded minc-toolkit, loaded minc-tools/mice-chihiro and tried the mincresample command again and it was successful on all files.