3dDeconvolve: mumap_chunk(): invalid pointer

AFNI Message Board
1

Hey, this is my first time to run afni analysis and the all the things look good expect this error. Is anyone can help? Thanks a lot.

*** Error in `3dDeconvolve’: munmap_chunk(): invalid pointer: 0x0000000001f007d8 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7b194)[0x7f29637d1194]
3dDeconvolve[0x628f2a]
3dDeconvolve[0x4c6875]
3dDeconvolve[0x417cad]
3dDeconvolve[0x42215a]
3dDeconvolve[0x428f41]
3dDeconvolve[0x436223]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f2963777b15]
3dDeconvolve[0x407ef9]
======= Memory map: ========
00400000-0092d000 r-xp 00000000 fd:00 3045477 /usr/local/afni/3dDeconvolve
00b2c000-00b77000 rw-p 0052c000 fd:00 3045477 /usr/local/afni/3dDeconvolve
00b77000-00bbf000 rw-p 00000000 00:00 0
01e9e000-01f76000 rw-p 00000000 00:00 0 [heap]
7f295802b000-7f2958040000 r-xp 00000000 fd:00 201326729 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f2958040000-7f295823f000 —p 00015000 fd:00 201326729 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f295823f000-7f2958240000 r–p 00014000 fd:00 201326729 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f2958240000-7f2958241000 rw-p 00015000 fd:00 201326729 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f2958241000-7f29625f9000 r–s 00000000 08:21 792455476 /data/wispic/caiying/YingMem/p999/subject_results/group.loc5small/subj.p999/p999.results/pb04.p999.r01.scale+tlrc.BRIK
7f29625f9000-7f296260f000 r-xp 00000000 fd:00 201330308 /usr/lib64/libpthread-2.17.so
7f296260f000-7f296280f000 —p 00016000 fd:00 201330308 /usr/lib64/libpthread-2.17.so
7f296280f000-7f2962810000 r–p 00016000 fd:00 201330308 /usr/lib64/libpthread-2.17.so
7f2962810000-7f2962811000 rw-p 00017000 fd:00 201330308 /usr/lib64/libpthread-2.17.so
7f2962811000-7f2962815000 rw-p 00000000 00:00 0
7f2962815000-7f296283c000 r-xp 00000000 fd:00 201397653 /usr/lib64/libexpat.so.1.6.0
7f296283c000-7f2962a3c000 —p 00027000 fd:00 201397653 /usr/lib64/libexpat.so.1.6.0
7f2962a3c000-7f2962a3e000 r–p 00027000 fd:00 201397653 /usr/lib64/libexpat.so.1.6.0
7f2962a3e000-7f2962a3f000 rw-p 00029000 fd:00 201397653 /usr/lib64/libexpat.so.1.6.0
7f2962a3f000-7f2962a60000 r-xp 00000000 fd:00 202814757 /usr/lib64/libxcb.so.1.1.0
7f2962a60000-7f2962c5f000 —p 00021000 fd:00 202814757 /usr/lib64/libxcb.so.1.1.0
7f2962c5f000-7f2962c60000 r–p 00020000 fd:00 202814757 /usr/lib64/libxcb.so.1.1.0
7f2962c60000-7f2962c61000 rw-p 00021000 fd:00 202814757 /usr/lib64/libxcb.so.1.1.0
7f2962c61000-7f2962c65000 r-xp 00000000 fd:00 201397353 /usr/lib64/libuuid.so.1.3.0
7f2962c65000-7f2962e64000 —p 00004000 fd:00 201397353 /usr/lib64/libuuid.so.1.3.0
7f2962e64000-7f2962e65000 r–p 00003000 fd:00 201397353 /usr/lib64/libuuid.so.1.3.0
7f2962e65000-7f2962e66000 rw-p 00004000 fd:00 201397353 /usr/lib64/libuuid.so.1.3.0
7f2962e66000-7f2962e68000 r-xp 00000000 fd:00 202814705 /usr/lib64/libXau.so.6.0.0
7f2962e68000-7f2963068000 —p 00002000 fd:00 202814705 /usr/lib64/libXau.so.6.0.0
7f2963068000-7f2963069000 r–p 00002000 fd:00 202814705 /usr/lib64/libXau.so.6.0.0
7f2963069000-7f296306a000 rw-p 00003000 fd:00 202814705 /usr/lib64/libXau.so.6.0.0
7f296306a000-7f2963073000 r-xp 00000000 fd:00 202846807 /usr/lib64/libXrender.so.1.3.0
7f2963073000-7f2963272000 —p 00009000 fd:00 202846807 /usr/lib64/libXrender.so.1.3.0
7f2963272000-7f2963273000 r–p 00008000 fd:00 202846807 /usr/lib64/libXrender.so.1.3.0
7f2963273000-7f2963274000 rw-p 00009000 fd:00 202846807 /usr/lib64/libXrender.so.1.3.0
7f2963274000-7f2963314000 r-xp 00000000 fd:00 201398737 /usr/lib64/libfreetype.so.6.10.0
7f2963314000-7f2963513000 —p 000a0000 fd:00 201398737 /usr/lib64/libfreetype.so.6.10.0
7f2963513000-7f2963519000 r–p 0009f000 fd:00 201398737 /usr/lib64/libfreetype.so.6.10.0
7f2963519000-7f296351a000 rw-p 000a5000 fd:00 201398737 /usr/lib64/libfreetype.so.6.10.0
7f296351a000-7f2963554000 r-xp 00000000 fd:00 202846812 /usr/lib64/libfontconfig.so.1.7.0
7f2963554000-7f2963753000 —p 0003a000 fd:00 202846812 /usr/lib64/libfontconfig.so.1.7.0
7f2963753000-7f2963755000 r–p 00039000 fd:00 202846812 /usr/lib64/libfontconfig.so.1.7.0
7f2963755000-7f2963756000 rw-p 0003b000 fd:00 202846812 /usr/lib64/libfontconfig.so.1.7.0
7f2963756000-7f296390d000 r-xp 00000000 fd:00 201328018 /usr/lib64/libc-2.17.so
7f296390d000-7f2963b0d000 —p 001b7000 fd:00 201328018 /usr/lib64/libc-2.17.so
7f2963b0d000-7f2963b11000 r–p 001b7000 fd:00 201328018 /usr/lib64/libc-2.17.so
7f2963b11000-7f2963b13000 rw-p 001bb000 fd:00 201328018 /usr/lib64/libc-2.17.so
7f2963b13000-7f2963b18000 rw-p 00000000 00:00 0
7f2963b18000-7f2963b1b000 r-xp 00000000 fd:00 201328024 /usr/lib64/libdl-2.17.so
7f2963b1b000-7f2963d1a000 —p 00003000 fd:00 201328024 /usr/lib64/libdl-2.17.so
7f2963d1a000-7f2963d1b000 r–p 00002000 fd:00 201328024 /usr/lib64/libdl-2.17.so
7f2963d1b000-7f2963d1c000 rw-p 00003000 fd:00 201328024 /usr/lib64/libdl-2.17.so
7f2963d1c000-7f2963e1d000 r-xp 00000000 fd:00 201328026 /usr/lib64/libm-2.17.so
7f2963e1d000-7f296401c000 —p 00101000 fd:00 201328026 /usr/lib64/libm-2.17.so
7f296401c000-7f296401d000 r–p 00100000 fd:00 201328026 /usr/lib64/libm-2.17.so
7f296401d000-7f296401e000 rw-p 00101000 fd:00 201328026 /usr/lib64/libm-2.17.so
7f296401e000-7f2964033000 r-xp 00000000 fd:00 201397320 /usr/lib64/libz.so.1.2.7
7f2964033000-7f2964232000 —p 00015000 fd:00 201397320 /usr/lib64/libz.so.1.2.7
7f2964232000-7f2964233000 r–p 00014000 fd:00 201397320 /usr/lib64/libz.so.1.2.7
7f2964233000-7f2964234000 rw-p 00015000 fd:00 201397320 /usr/lib64/libz.so.1.2.7
7f2964234000-7f296425a000 r-xp 00000000 fd:00 229647384 /usr/lib64/libpng12.so.0.50.0
Fatal Signal 6 (SIGABRT) received
SYM_expand_ranges
read_glt_matrix
read_input_data
initialize_program
3dDeconvolve main
Bottom of Debug Stack
** Command line was:
3dDeconvolve -input pb04.p999.r01.scale+tlrc.HEAD -censor motion_p999_censor.1D -polort 7 -num_stimts 12 -stim_times 1 stimuli/5location_loc1.txt ‘BLOCK(12,1)’ -stim_label 1 loc1 -stim_times 2 stimuli/5location_loc2.txt ‘BLOCK(12,1)’ -stim_label 2 loc2 -stim_times 3 stimuli/5location_loc3.txt ‘BLOCK(12,1)’ -stim_label 3 loc3 -stim_times 4 stimuli/5location_loc4.txt ‘BLOCK(12,1)’ -stim_label 4 loc4 -stim_times 5 stimuli/5location_loc5.txt ‘BLOCK(12,1)’ -stim_label 5 loc5 -stim_times 6 stimuli/5location_rest.txt ‘BLOCK(12,1)’ -stim_label 6 rest -stim_file 7 ‘motion_demean.1D[0]’ -stim_base 7 -stim_label 7 roll -stim_file 8 ‘motion_demean.1D[1]’ -stim_base 8 -stim_label 8 pitch -stim_file 9 ‘motion_demean.1D[2]’ -stim_base 9 -stim_label 9 yaw -stim_file 10 ‘motion_demean.1D[3]’ -stim_base 10 -stim_label 10 dS -stim_file 11 ‘motion_demean.1D[4]’ -stim_base 11 -stim_label 11 dL -stim_file 12 ‘motion_demean.1D[5]’ -stim_base 12 -stim_label 12 dP -gltsym ‘SYM: loc1 - rest’ -glt_label 1 c1 -gltsym ‘SYM: loc2 - rest’ -glt_label 2 c2 -gltsym ‘SYM: loc3 - rest’ -glt_label 3 c3 -gltsym ‘SYM: loc4 - rest’ -glt_label 4 c4 -gltsym ‘SYM: loc5 - rest’ -glt_label 5 c5 -gltsym ‘SYM: 0.2loc1 + 0.2loc2 + 0.2loc3 + 0.2loc4 +0.2*loc5 - rest’ -glt_label 6 c6 -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.p999 -errts errts.p999 -bucket stats.p999
** AFNI version = AFNI_16.2.01 Compile date = Jul 9 2016
** [[Precompiled binary linux_openmp_64: Jul 9 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=1783 bytes=399095

2

There was a problem with having the ‘+’ and ‘-’ separated
from the labels or scalars in the GLTs that was fixed just a
couple of weeks after the date of your AFNI binaries (from
last July).

Please update to anything as new as July 25, 2016 and
try again.

Or, remove the spaces from the GLT labels, as in:

-gltsym 'SYM: loc1 -rest' -glt_label 1 c1  \
-gltsym 'SYM: loc2 -rest' -glt_label 2 c2  \
-gltsym 'SYM: loc3 -rest' -glt_label 3 c3  \
-gltsym 'SYM: loc4 -rest' -glt_label 4 c4  \
-gltsym 'SYM: loc5 -rest' -glt_label 5 c5  \
-gltsym 'SYM: 0.2*loc1 +0.2*loc2 +0.2*loc3 +0.2*loc4 +0.2*loc5 -rest' -glt_label 6 c6

Please let me know if you have any questions about that.

  • rick