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January 11, 2018 03:50PM avatar
Hello AFNI friends,

I was trying to experiment with some of the network(ish) tools in AFNI. I ran 3dECM with the following syntax:

3dECM -fecm -mask /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz -prefix 150926_20176_3dECM.nii.gz filt_denoised_func_data_nonaggr_MNI_wmcsf.nii.gz
[Which is a resting state scan, denoised with ICA-AROMA with wm, csf, and motion nuisance regressors (also bandpassing)...

And I got the following out:

++ 3dECM: AFNI version=AFNI_17.3.09 (Dec 22 2017) [64-bit]
++ 228453 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with FECM (sparsity=100.000%,thresh=-1.200,
  scale=0.500, shift=1.000, max_iter=10000, eps=0.000, binary=0)
creating output bucket(150926_20176_3dECM.nii.gz)
 + creating output dataset in memory
*** Error in `3dECM': munmap_chunk(): invalid pointer: 0x00000000004072eb ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fa0239437e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fa023950698]
3dECM[0x44fb76]
3dECM[0x40b760]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fa0238ec830]
3dECM[0x408169]
======= Memory map: ========
00400000-008f0000 r-xp 00000000 09:01 4203479                            /usr/local/pkg/afni/3dECM
00aef000-00b39000 rw-p 004ef000 09:01 4203479                            /usr/local/pkg/afni/3dECM
00b39000-00b94000 rw-p 00000000 00:00 0
01d5b000-31ccd000 rw-p 00000000 00:00 0                                  [heap]
7fa0218d7000-7fa0218ed000 r-xp 00000000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa0218ed000-7fa021aec000 ---p 00016000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa021aec000-7fa021aed000 r--p 00015000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa021aed000-7fa021aee000 rw-p 00016000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa021aee000-7fa021af9000 r-xp 00000000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021af9000-7fa021cf8000 ---p 0000b000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021cf8000-7fa021cf9000 r--p 0000a000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021cf9000-7fa021cfa000 rw-p 0000b000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021cfa000-7fa021d00000 rw-p 00000000 00:00 0
7fa021d00000-7fa021d0b000 r-xp 00000000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021d0b000-7fa021f0a000 ---p 0000b000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021f0a000-7fa021f0b000 r--p 0000a000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021f0b000-7fa021f0c000 rw-p 0000b000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021f0c000-7fa021f22000 r-xp 00000000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa021f22000-7fa022121000 ---p 00016000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa022121000-7fa022122000 r--p 00015000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa022122000-7fa022123000 rw-p 00016000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa022123000-7fa022125000 rw-p 00000000 00:00 0
7fa022125000-7fa02212d000 r-xp 00000000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02212d000-7fa02232c000 ---p 00008000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02232c000-7fa02232d000 r--p 00007000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02232d000-7fa02232e000 rw-p 00008000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02232e000-7fa022333000 r-xp 00000000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022333000-7fa022532000 ---p 00005000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022532000-7fa022533000 r--p 00004000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022533000-7fa022534000 rw-p 00005000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022534000-7fa02255a000 r-xp 00000000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02255a000-7fa02275a000 ---p 00026000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02275a000-7fa02275c000 r--p 00026000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02275c000-7fa02275d000 rw-p 00028000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02275d000-7fa02277e000 r-xp 00000000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02277e000-7fa02297d000 ---p 00021000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02297d000-7fa02297e000 r--p 00020000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02297e000-7fa02297f000 rw-p 00021000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02297f000-7fa022983000 r-xp 00000000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022983000-7fa022b82000 ---p 00004000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022b82000-7fa022b83000 r--p 00003000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022b83000-7fa022b84000 rw-p 00004000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022b84000-7fa022b86000 r-xp 00000000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022b86000-7fa022d86000 ---p 00002000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022d86000-7fa022d87000 r--p 00002000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022d87000-7fa022d88000 rw-p 00003000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022d88000-7fa022d91000 r-xp 00000000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022d91000-7fa022f90000 ---p 00009000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022f90000-7fa022f91000 r--p 00008000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022f91000-7fa022f92000 rw-p 00009000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022f92000-7fa023036000 r-xp 00000000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa023036000-7fa023235000 ---p 000a4000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa023235000-7fa02323b000 r--p 000a3000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa02323b000-7fa02323c000 rw-p 000a9000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa02323c000-7fa023279000 r-xp 00000000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa023279000-7fa023478000 ---p 0003d000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa023478000-7fa02347a000 r--p 0003c000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa02347a000-7fa02347f000 rw-p 0003e000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa02347f000-7fa023497000 r-xp 00000000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023497000-7fa023696000 ---p 00018000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023696000-7fa023697000 r--p 00017000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023697000-7fa023698000 rw-p 00018000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023698000-7fa02369c000 rw-p 00000000 00:00 0
7fa02369c000-7fa0236ca000 r-xp 00000000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0236ca000-7fa0238ca000 ---p 0002e000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0238ca000-7fa0238cb000 r--p 0002e000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0238cb000-7fa0238cc000 rw-p 0002f000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0238cc000-7fa023a8c000 r-xp 00000000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023a8c000-7fa023c8c000 ---p 001c0000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023c8c000-7fa023c90000 r--p 001c0000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023c90000-7fa023c92000 rw-p 001c4000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023c92000-7fa023c96000 rw-p 00000000 00:00 0
7fa023c96000-7fa023c99000 r-xp 00000000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023c99000-7fa023e98000 ---p 00003000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023e98000-7fa023e99000 r--p 00002000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023e99000-7fa023e9a000 rw-p 00003000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023e9a000-7fa023fa2000 r-xp 00000000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa023fa2000-7fa0241a1000 ---p 00108000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa0241a1000-7fa0241a2000 r--p 00107000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa0241a2000-7fa0241a3000 rw-p 00108000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa0241a3000-7fa0241bc000 r-xp 00000000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0241bc000-7fa0243bb000 ---p 00019000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0243bb000-7fa0243bc000 r--p 00018000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0243bc000-7fa0243bd000 rw-p 00019000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0243bd000-7fa0243e1000 r-xp 00000000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0243e1000-7fa0245e0000 ---p 00024000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0245e0000-7fa0245e1000 r--p 00023000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0245e1000-7fa0245e2000 rw-p 00024000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0245e2000-7fa024717000 r-xp 00000000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa024717000-7fa024917000 ---p 00135000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa024917000-7fa024918000 r--p 00135000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa024918000-7fa02491c000 rw-p 00136000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa02491c000-7fa024932000 r-xp 00000000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024932000-7fa024b31000 ---p 00016000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024b31000-7fa024b32000 r--p 00015000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024b32000-7fa024b33000 rw-p 00016000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024b33000-7fa024b36000 rw-p 00000000 00:00 0
7fa024b36000-7fa024b3d000 r-xp 00000000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024b3d000-7fa024d3c000 ---p 00007000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024d3c000-7fa024d3d000 r--p 00006000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024d3d000-7fa024d3e000 rw-p 00007000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024d3e000-7fa024d56000 r-xp 00000000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024d56000-7fa024f55000 ---p 00018000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024f55000-7fa024f56000 r--p 00017000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024f56000-7fa024f57000 rw-p 00018000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024f57000-7fa024f68000 r-xp 00000000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa024f68000-7fa025167000 ---p 00011000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa025167000-7fa025168000 r--p 00010000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa025168000-7fa025169000 rw-p 00011000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa025169000-7fa025179000 r-xp 00000000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa025179000-7fa025379000 ---p 00010000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa025379000-7fa02537a000 r--p 00010000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa02537a000-7fa02537b000 rw-p 00011000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa02537b000-7fa025383000 r-xp 00000000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025383000-7fa025582000 ---p 00008000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025582000-7fa025583000 r--p 00007000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025583000-7fa025584000 rw-p 00008000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025584000-7fa025598000 r-xp 00000000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025598000-7fa025797000 ---p 00014000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025797000-7fa025798000 r--p 00013000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025798000-7fa025799000 rw-p 00014000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025799000-7fa0257fb000 r-xp 00000000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa0257fb000-7fa0259fb000 ---p 00062000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa0259fb000-7fa0259fc000 r--p 00062000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa0259fc000-7fa025a01000 rw-p 00063000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa025a01000-7fa025a02000 rw-p 00000000 00:00 0
7fa025a02000-7fa025a28000 r-xp 00000000 09:01 9441205                    /lib/x86_64-linux-gnu/ld-2.23.so
7fa025bf3000-7fa025bff000 rw-p 00000000 00:00 0
7fa025c24000-7fa025c27000 rw-p 00000000 00:00 0
7fa025c27000-7fa025c28000 r--p 00025000 09:01 9441205                    /lib/x86_64-linux-gnu/ld-2.23.so
7fa025c28000-7fa025c29000 rw-p 00026000 09:01 9441205                    /lib/x86_64-linux-gnu/ld-2.23.so
7fa025c29000-7fa025c2a000 rw-p 00000000 00:00 0
7ffc4ad1c000-7ffc4ad3d000 rw-p 00000000 00:00 0                          [stack]
7ffc4adee000-7ffc4adf0000 r--p 00000000 00:00 0                          [vvar]
7ffc4adf0000-7ffc4adf2000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Fatal Signal 6 (SIGABRT) received
  3dECM main
 Bottom of Debug Stack
** Command line was:
3dECM -fecm -mask /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz -prefix 150926_20176_3dECM.nii.gz filt_denoised_func_data_nonaggr_MNI_wmcsf.nii.gz
** AFNI version = AFNI_17.3.09  Compile date = Dec 22 2017
** [[Precompiled binary linux_openmp_64: Dec 22 2017]]
** 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.
** Crash log is appended to file /home/jamielh/.afni.crashlog

I'm no expert, but that didn't look good. Anyone else run into similar issues? Did I somehow break my server's memory? [My IT folks are really going to be pissed at me if so... eye rolling smiley)

Thanks in advance for any thoughts!
Jamie.
Subject Author Posted

3dECM crash

jamielarshanson January 11, 2018 03:50PM

Re: 3dECM crash

jamielarshanson January 18, 2018 03:38PM

Re: 3dECM crash

ccraddock January 20, 2018 02:10PM



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