External Email - Use Caution Hello FreeSurfer Developers,
I'm attempting to generate filled.mgz using the mri_fill -a */ponscc.cut.log -xform */talairach.lta -segementation aseg.auto_noCCseg.mgz wm.mgz filled.mgz Error : *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 *** And before the error: INFO: Using /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/transforms/talairach.lta and its offset for Talairach volume ... using segmentation /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.26345 -0.00883 0.01215 -37.76160; 0.05445 1.62947 0.37797 -140.90414; -0.00773 -0.25421 1.23906 -2.18153; 0.00000 0.00000 0.00000 1.00000; reading segmented volume /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz voxel to talairach voxel transform 1.26345 -0.00883 0.01215 -37.76160; 0.05445 1.62947 0.37797 -140.90414; -0.00773 -0.25421 1.23906 -2.18153; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 108, 153) --> (3.0, 25.0, 20.0) Looking for area (min, max) = (350, 1400) area[0] = 2589 (min = 350, max = 1400), aspect = 1.11 (min = 0.10, max = 0.75) need search nearby using seed (125, 108, 153), TAL = (3.0, 25.0, 20.0) The details of bug is attached in the attachment. The data come from a macaque.But I can use ""mri_fill" with -CV -PV to generate filled.mgz I've searched the list and no similar error have been reported. Looking forward to your reply.
mri_fill -a $FS_dir/scripts/ponscc.cut.log -xform $FSM_dir/transforms/talairach.lta -segmentation $FSM_dir/aseg.auto_noCCseg.mgz $FSM_dir/wm.mgz $FSM_dir/filled.mgz logging cutting plane coordinates to /home/qding/FBIP/pipeline/KM_test/2//KM002/scripts/ponscc.cut.log... INFO: Using /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/transforms/talairach.lta and its offset for Talairach volume ... using segmentation /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.26345 -0.00883 0.01215 -37.76160; 0.05445 1.62947 0.37797 -140.90414; -0.00773 -0.25421 1.23906 -2.18153; 0.00000 0.00000 0.00000 1.00000; reading segmented volume /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz voxel to talairach voxel transform 1.26345 -0.00883 0.01215 -37.76160; 0.05445 1.62947 0.37797 -140.90414; -0.00773 -0.25421 1.23906 -2.18153; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 108, 153) --> (3.0, 25.0, 20.0) Looking for area (min, max) = (350, 1400) area[0] = 2589 (min = 350, max = 1400), aspect = 1.11 (min = 0.10, max = 0.75) need search nearby using seed (125, 108, 153), TAL = (3.0, 25.0, 20.0) *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 *** ======= Backtrace: ========= /usr/lib64/libc.so.6(+0x81299)[0x7f22d8d36299] mri_fill[0x52ffd9] mri_fill[0x43305b] mri_fill[0x4330a9] mri_fill[0x4130ce] /usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f22d8cd7555] mri_fill[0x419617] ======= Memory map: ======== 00400000-006cc000 r-xp 00000000 00:26 5349298185 /share/apps/imaging/freesurfer-7.1.0/bin/mri_fill 008cb000-008d3000 r--p 002cb000 00:26 5349298185 /share/apps/imaging/freesurfer-7.1.0/bin/mri_fill 008d3000-008fe000 rw-p 002d3000 00:26 5349298185 /share/apps/imaging/freesurfer-7.1.0/bin/mri_fill 008fe000-0090f000 rw-p 00000000 00:00 0 01268000-019e2000 rw-p 00000000 00:00 0 [heap] 7f22c0000000-7f22c0021000 rw-p 00000000 00:00 0 7f22c0021000-7f22c4000000 ---p 00000000 00:00 0 7f22c5148000-7f22c6149000 rw-p 00000000 00:00 0 7f22ca14a000-7f22d214f000 rw-p 00000000 00:00 0 7f22d214f000-7f22d8692000 r--p 00000000 08:05 86890 /usr/lib/locale/locale-archive 7f22d8692000-7f22d869e000 r-xp 00000000 08:05 3522256 /usr/lib64/libnss_ldap.so.2 7f22d869e000-7f22d889d000 ---p 0000c000 08:05 3522256 /usr/lib64/libnss_ldap.so.2 7f22d889d000-7f22d889e000 r--p 0000b000 08:05 3522256 /usr/lib64/libnss_ldap.so.2 7f22d889e000-7f22d889f000 rw-p 0000c000 08:05 3522256 /usr/lib64/libnss_ldap.so.2 7f22d889f000-7f22d88ab000 r-xp 00000000 08:05 87232 /usr/lib64/libnss_files-2.17.so 7f22d88ab000-7f22d8aaa000 ---p 0000c000 08:05 87232 /usr/lib64/libnss_files-2.17.so 7f22d8aaa000-7f22d8aab000 r--p 0000b000 08:05 87232 /usr/lib64/libnss_files-2.17.so 7f22d8aab000-7f22d8aac000 rw-p 0000c000 08:05 87232 /usr/lib64/libnss_files-2.17.so 7f22d8aac000-7f22d8ab2000 rw-p 00000000 00:00 0 7f22d8ab2000-7f22d8ab4000 r-xp 00000000 08:05 86619 /usr/lib64/libfreebl3.so 7f22d8ab4000-7f22d8cb3000 ---p 00002000 08:05 86619 /usr/lib64/libfreebl3.so 7f22d8cb3000-7f22d8cb4000 r--p 00001000 08:05 86619 /usr/lib64/libfreebl3.so 7f22d8cb4000-7f22d8cb5000 rw-p 00002000 08:05 86619 /usr/lib64/libfreebl3.so 7f22d8cb5000-7f22d8e78000 r-xp 00000000 08:05 6771608 /usr/lib64/libc-2.17.so 7f22d8e78000-7f22d9078000 ---p 001c3000 08:05 6771608 /usr/lib64/libc-2.17.so 7f22d9078000-7f22d907c000 r--p 001c3000 08:05 6771608 /usr/lib64/libc-2.17.so 7f22d907c000-7f22d907e000 rw-p 001c7000 08:05 6771608 /usr/lib64/libc-2.17.so 7f22d907e000-7f22d9083000 rw-p 00000000 00:00 0 7f22d9083000-7f22d9098000 r-xp 00000000 08:05 117 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f22d9098000-7f22d9297000 ---p 00015000 08:05 117 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f22d9297000-7f22d9298000 r--p 00014000 08:05 117 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f22d9298000-7f22d9299000 rw-p 00015000 08:05 117 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f22d9299000-7f22d9382000 r-xp 00000000 08:05 87565 /usr/lib64/libstdc++.so.6.0.19 7f22d9382000-7f22d9581000 ---p 000e9000 08:05 87565 /usr/lib64/libstdc++.so.6.0.19 7f22d9581000-7f22d9589000 r--p 000e8000 08:05 87565 /usr/lib64/libstdc++.so.6.0.19 7f22d9589000-7f22d958b000 rw-p 000f0000 08:05 87565 /usr/lib64/libstdc++.so.6.0.19 7f22d958b000-7f22d95a0000 rw-p 00000000 00:00 0 7f22d95a0000-7f22d95a7000 r-xp 00000000 08:05 87250 /usr/lib64/librt-2.17.so 7f22d95a7000-7f22d97a6000 ---p 00007000 08:05 87250 /usr/lib64/librt-2.17.so 7f22d97a6000-7f22d97a7000 r--p 00006000 08:05 87250 /usr/lib64/librt-2.17.so 7f22d97a7000-7f22d97a8000 rw-p 00007000 08:05 87250 /usr/lib64/librt-2.17.so 7f22d97a8000-7f22d97b0000 r-xp 00000000 08:05 6771612 /usr/lib64/libcrypt-2.17.so 7f22d97b0000-7f22d99af000 ---p 00008000 08:05 6771612 /usr/lib64/libcrypt-2.17.so 7f22d99af000-7f22d99b0000 r--p 00007000 08:05 6771612 /usr/lib64/libcrypt-2.17.so 7f22d99b0000-7f22d99b1000 rw-p 00008000 08:05 6771612 /usr/lib64/libcrypt-2.17.so 7f22d99b1000-7f22d99df000 rw-p 00000000 00:00 0 7f22d99df000-7f22d9a04000 r-xp 00000000 08:05 88534 /usr/lib64/libgomp.so.1.0.0 7f22d9a04000-7f22d9c03000 ---p 00025000 08:05 88534 /usr/lib64/libgomp.so.1.0.0 7f22d9c03000-7f22d9c04000 r--p 00024000 08:05 88534 /usr/lib64/libgomp.so.1.0.0 7f22d9c04000-7f22d9c05000 rw-p 00025000 08:05 88534 /usr/lib64/libgomp.so.1.0.0 7f22d9c05000-7f22d9d06000 r-xp 00000000 08:05 86893 /usr/lib64/libm-2.17.so 7f22d9d06000-7f22d9f05000 ---p 00101000 08:05 86893 /usr/lib64/libm-2.17.so 7f22d9f05000-7f22d9f06000 r--p 00100000 08:05 86893 /usr/lib64/libm-2.17.so 7f22d9f06000-7f22d9f07000 rw-p 00101000 08:05 86893 /usr/lib64/libm-2.17.so 7f22d9f07000-7f22d9f09000 r-xp 00000000 08:05 86891 /usr/lib64/libdl-2.17.so 7f22d9f09000-7f22da109000 ---p 00002000 08:05 86891 /usr/lib64/libdl-2.17.so 7f22da109000-7f22da10a000 r--p 00002000 08:05 86891 /usr/lib64/libdl-2.17.so 7f22da10a000-7f22da10b000 rw-p 00003000 08:05 86891 /usr/lib64/libdl-2.17.so 7f22da10b000-7f22da122000 r-xp 00000000 08:05 87245 /usr/lib64/libpthread-2.17.so 7f22da122000-7f22da321000 ---p 00017000 08:05 87245 /usr/lib64/libpthread-2.17.so 7f22da321000-7f22da322000 r--p 00016000 08:05 87245 /usr/lib64/libpthread-2.17.so 7f22da322000-7f22da323000 rw-p 00017000 08:05 87245 /usr/lib64/libpthread-2.17.so 7f22da323000-7f22da327000 rw-p 00000000 00:00 0 7f22da327000-7f22da343000 r-xp 00000000 08:05 5258267 /opt/minc/1.9.18/lib/libz.so.1.2.11 7f22da343000-7f22da542000 ---p 0001c000 08:05 5258267 /opt/minc/1.9.18/lib/libz.so.1.2.11 7f22da542000-7f22da543000 r--p 0001b000 08:05 5258267 /opt/minc/1.9.18/lib/libz.so.1.2.11 7f22da543000-7f22da544000 rw-p 0001c000 08:05 5258267 /opt/minc/1.9.18/lib/libz.so.1.2.11 7f22da544000-7f22da566000 r-xp 00000000 08:05 6771601 /usr/lib64/ld-2.17.so 7f22da72b000-7f22da733000 rw-p 00000000 00:00 0 7f22da75f000-7f22da765000 rw-p 00000000 00:00 0 7f22da765000-7f22da766000 r--p 00021000 08:05 6771601 /usr/lib64/ld-2.17.so 7f22da766000-7f22da767000 rw-p 00022000 08:05 6771601 /usr/lib64/ld-2.17.so 7f22da767000-7f22da768000 rw-p 00000000 00:00 0 7ffcb9086000-7ffcb90a8000 rw-p 00000000 00:00 0 [stack] 7ffcb917d000-7ffcb917f000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
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