Hard to say. Can you send the full terminal output? You can just run it like: mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 10000 1.3 mc-z.abs.13.jls --sim-sign abs --overwrite |& glmfitsim.log Then send me the log file. doug
On 04/11/2012 05:14 PM, Jeff Sadino wrote:
Hello FreeSurfers,
I ran the following command: mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 10000 1.3 mc-z.abs.13.jls --sim-sign abs --overwrite
When it gets to the part to do mri_segstats, it throws this error: 0 1*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2f302488 ***
I see this person had a similar problem: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15423.html
All of my other mri_glmfit-sim commands have worked fine. Is this a bug in mri_segstats? I am rerunning it again to see if it is duplicatable.
The rest of the error log looks like this: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.sig.ocn.mgh --exclude 0 --i rhFwhm12Sig13/y.mgh --avgwf rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.20258 sysname Linux hostname calypso machine i686 user ash Loading rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.sig.ocn.mgh Loading rhFwhm12Sig13/y.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 3 segmentations Computing statistics for each segmentation 1 1 1327 1327 2 2 1403 1403
Reporting on 2 segmentations Computing spatial average of each frame 0 1*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2f302488 *** ======= Backtrace: ========= /lib/i386-linux-gnu/libc.so.6(+0x6b961)[0xb761d961] /lib/i386-linux-gnu/libc.so.6(+0x6e15d)[0xb762015d] /lib/i386-linux-gnu/libc.so.6(__libc_malloc+0x63)[0xb7621f53] /lib/i386-linux-gnu/libc.so.6(+0x5c2b8)[0xb760e2b8] /lib/i386-linux-gnu/libc.so.6(fopen64+0x2c)[0xb76109cc] mri_segstats(vfprintf+0x3e9e)[0x80526d6] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0xb75c8e37] mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791] ======= Memory map: ======== 08048000-087f2000 r-xp 00000000 00:00 0 087f2000-2e568000 rwxp 00000000 00:00 0 2f288000-2f34e000 rwxp 00000000 00:00 0 [heap] b2f00000-b2f21000 rwxp 00000000 00:00 0 b2f21000-b3000000 ---p 00000000 00:00 0 b30e5000-b74d1000 rwxp 00000000 00:00 0 b7572000-b757c000 r-xp 00000000 08:15 11666287 /lib/i386-linux-gnu/libnss_files-2.13.so http://libnss_files-2.13.so b757c000-b757d000 r-xp 00009000 08:15 11666287 /lib/i386-linux-gnu/libnss_files-2.13.so http://libnss_files-2.13.so b757d000-b757e000 rwxp 0000a000 08:15 11666287 /lib/i386-linux-gnu/libnss_files-2.13.so http://libnss_files-2.13.so b757e000-b7591000 r-xp 00000000 08:15 11666281 /lib/i386-linux-gnu/libnsl-2.13.so http://libnsl-2.13.so b7591000-b7592000 r-xp 00012000 08:15 11666281 /lib/i386-linux-gnu/libnsl-2.13.so http://libnsl-2.13.so b7592000-b7593000 rwxp 00013000 08:15 11666281 /lib/i386-linux-gnu/libnsl-2.13.so http://libnsl-2.13.so b7593000-b7595000 rwxp 00000000 00:00 0 b75b0000-b75b2000 rwxp 00000000 00:00 0 b75b2000-b770c000 r-xp 00000000 08:15 11666241 /lib/i386-linux-gnu/libc-2.13.so http://libc-2.13.so b770c000-b770d000 ---p 0015a000 08:15 11666241 /lib/i386-linux-gnu/libc-2.13.so http://libc-2.13.so b770d000-b770f000 r-xp 0015a000 08:15 11666241 /lib/i386-linux-gnu/libc-2.13.so http://libc-2.13.so b770f000-b7710000 rwxp 0015c000 08:15 11666241 /lib/i386-linux-gnu/libc-2.13.so http://libc-2.13.so b7710000-b7714000 rwxp 00000000 00:00 0 b7714000-b772e000 r-xp 00000000 08:15 11666269 /lib/i386-linux-gnu/libgcc_s.so.1 b772e000-b772f000 r-xp 00019000 08:15 11666269 /lib/i386-linux-gnu/libgcc_s.so.1 b772f000-b7730000 rwxp 0001a000 08:15 11666269 /lib/i386-linux-gnu/libgcc_s.so.1 b7730000-b7754000 r-xp 00000000 08:15 11666278 /lib/i386-linux-gnu/libm-2.13.so http://libm-2.13.so b7754000-b7755000 r-xp 00023000 08:15 11666278 /lib/i386-linux-gnu/libm-2.13.so http://libm-2.13.so b7755000-b7756000 rwxp 00024000 08:15 11666278 /lib/i386-linux-gnu/libm-2.13.so http://libm-2.13.so b7756000-b7835000 r-xp 00000000 08:15 24387549 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.14 b7835000-b7839000 r-xp 000de000 08:15 24387549 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.14 b7839000-b783a000 rwxp 000e2000 08:15 24387549 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.14 b783a000-b7841000 rwxp 00000000 00:00 0 b7841000-b7856000 r-xp 00000000 08:15 11666306 /lib/i386-linux-gnu/libpthread-2.13.so http://libpthread-2.13.so b7856000-b7857000 r-xp 00015000 08:15 11666306 /lib/i386-linux-gnu/libpthread-2.13.so http://libpthread-2.13.so b7857000-b7858000 rwxp 00016000 08:15 11666306 /lib/i386-linux-gnu/libpthread-2.13.so http://libpthread-2.13.so b7858000-b785a000 rwxp 00000000 00:00 0 b785a000-b785c000 r-xp 00000000 08:15 11666251 /lib/i386-linux-gnu/libdl-2.13.so http://libdl-2.13.so b785c000-b785d000 r-xp 00001000 08:15 11666251 /lib/i386-linux-gnu/libdl-2.13.so http://libdl-2.13.so b785d000-b785e000 rwxp 00002000 08:15 11666251 /lib/i386-linux-gnu/libdl-2.13.so http://libdl-2.13.so b785e000-b785f000 rwxp 00000000 00:00 0 b785f000-b7867000 r-xp 00000000 08:15 11666247 /lib/i386-linux-gnu/libcrypt-2.13.so http://libcrypt-2.13.so b7867000-b7868000 r-xp 00007000 08:15 11666247 /lib/i386-linux-gnu/libcrypt-2.13.so http://libcrypt-2.13.so b7868000-b7869000 rwxp 00008000 08:15 11666247 /lib/i386-linux-gnu/libcrypt-2.13.so http://libcrypt-2.13.so b7869000-b7890000 rwxp 00000000 00:00 0 b7890000-b78a3000 r-xp 00000000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78a3000-b78a4000 r-xp 00012000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78a4000-b78a5000 rwxp 00013000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78ac000-b78b5000 r-xp 00000000 08:15 11666291 /lib/i386-linux-gnu/libnss_nis-2.13.so http://libnss_nis-2.13.so b78b5000-b78b6000 r-xp 00008000 08:15 11666291 /lib/i386-linux-gnu/libnss_nis-2.13.so http://libnss_nis-2.13.so b78b6000-b78b7000 rwxp 00009000 08:15 11666291 /lib/i386-linux-gnu/libnss_nis-2.13.so http://libnss_nis-2.13.so b78b7000-b78bd000 r-xp 00000000 08:15 11666283 /lib/i386-linux-gnu/libnss_compat-2.13.so http://libnss_compat-2.13.so b78bd000-b78be000 r-xp 00005000 08:15 11666283 /lib/i386-linux-gnu/libnss_compat-2.13.so http://libnss_compat-2.13.so b78be000-b78bf000 rwxp 00006000 08:15 11666283 /lib/i386-linux-gnu/libnss_compat-2.13.so http://libnss_compat-2.13.so b78bf000-b78c2000 rwxp 00000000 00:00 0 b78c2000-b78de000 r-xp 00000000 08:15 11666228 /lib/i386-linux-gnu/ld-2.13.so http://ld-2.13.so b78de000-b78df000 r-xp 0001b000 08:15 11666228 /lib/i386-linux-gnu/ld-2.13.so http://ld-2.13.so b78df000-b78e0000 rwxp 0001c000 08:15 11666228 /lib/i386-linux-gnu/ld-2.13.so http://ld-2.13.so b78e0000-b78e1000 r-xp 00000000 00:00 0 [vdso] bf87f000-bf8a1000 rwxp 00000000 00:00 0 [stack]
Writing to rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.y.ocn.dat Abort
Thank you for your help! Jeff Sadino
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer