Hi
Thanks for your reply.
I am rerunning some old analyses and everything works fine except the segmentation for this one subject (we have enough RAM to support the analysis, as advised by our technical staff). This problem has started happening only recently; the old GLMs (including
parametric modulator analysis with more regressors) gave no errors for this subject, suggesting there's nothing wrong with this subject's extracted structural scan.
I have tried running only FAST using extracted structural as an input and the following error comes up:
/usr/local/fsl-5/bin/fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -o /studies/2009/BBCEO/converted/BrainBank_SONA/BrainBank_un0009_HYA/co20120309_104747t1mprtraisop2TI1100FatSuprs023a1001_brain_0 /studies/2009/BBCEO/converted/BrainBank_SONA/BrainBank_un0009_HYA/co20120309_104747t1mprtraisop2TI1100FatSuprs023a1001_brain_0.37
*** glibc detected *** /usr/local/fsl-5/bin/fast: free(): invalid pointer: 0x00007f615f811010 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7c856)[0x7f61912b2856]
/usr/local/fsl-5/bin/fast[0x4417d8]
/usr/local/fsl-5/bin/fast[0x4bd1c8]
/usr/local/fsl-5/bin/fast[0x4bd308]
/usr/local/fsl-5/bin/fast[0x4bd339]
/usr/local/fsl-5/bin/fast[0x420f6e]
/usr/local/fsl-5/bin/fast[0x41e8c4]
/usr/local/fsl-5/bin/fast[0x41ebd9]
/usr/local/fsl-5/bin/fast[0x41ff87]
/usr/local/fsl-5/bin/fast[0x408a80]
/usr/local/fsl-5/bin/fast[0x405c5e]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f619125a6c5]
/usr/local/fsl-5/bin/fast[0x406101]
======= Memory map: ========
00400000-005eb000 r-xp 00000000 08:01 3671935 /usr/local/fsl-5.0.4/bin/fast
007ea000-007eb000 r--p 001ea000 08:01 3671935 /usr/local/fsl-5.0.4/bin/fast
007eb000-007ec000 rw-p 001eb000 08:01 3671935 /usr/local/fsl-5.0.4/bin/fast
007ec000-007ed000 rw-p 00000000 00:00 0
02566000-02599000 rw-p 00000000 00:00 0 [heap]
7f615d240000-7f6191236000 rw-p 00000000 00:00 0
7f6191236000-7f61913d3000 r-xp 00000000 08:01 3547565 /lib64/libc-2.15.so
7f61913d3000-7f61915d2000 ---p 0019d000 08:01 3547565 /lib64/libc-2.15.so
7f61915d2000-7f61915d6000 r--p 0019c000 08:01 3547565 /lib64/libc-2.15.so
7f61915d6000-7f61915d8000 rw-p 001a0000 08:01 3547565 /lib64/libc-2.15.so
7f61915d8000-7f61915dc000 rw-p 00000000 00:00 0
7f61915dc000-7f61915f1000 r-xp 00000000 08:01 3034461 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libgcc_s.so.1
7f61915f1000-7f61917f0000 ---p 00015000 08:01 3034461 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libgcc_s.so.1
7f61917f0000-7f61917f1000 r--p 00014000 08:01 3034461 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libgcc_s.so.1
7f61917f1000-7f61917f2000 rw-p 00015000 08:01 3034461 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libgcc_s.so.1
7f61917f2000-7f61918df000 r-xp 00000000 08:01 3547553 /lib64/libm-2.15.so
7f61918df000-7f6191ade000 ---p 000ed000 08:01 3547553 /lib64/libm-2.15.so
7f6191ade000-7f6191adf000 r--p 000ec000 08:01 3547553 /lib64/libm-2.15.so
7f6191adf000-7f6191ae0000 rw-p 000ed000 08:01 3547553 /lib64/libm-2.15.so
7f6191ae0000-7f6191bca000 r-xp 00000000 08:01 3034330 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libstdc++.so.6.0.17
7f6191bca000-7f6191dc9000 ---p 000ea000 08:01 3034330 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libstdc++.so.6.0.17
7f6191dc9000-7f6191dd1000 r--p 000e9000 08:01 3034330 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libstdc++.so.6.0.17
7f6191dd1000-7f6191dd3000 rw-p 000f1000 08:01 3034330 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.7.3/libstdc++.so.6.0.17
7f6191dd3000-7f6191de8000 rw-p 00000000 00:00 0
7f6191de8000-7f6191dff000 r-xp 00000000 08:01 3281834 /lib64/libz.so.1.2.7
7f6191dff000-7f6191ffe000 ---p 00017000 08:01 3281834 /lib64/libz.so.1.2.7
7f6191ffe000-7f6191fff000 r--p 00016000 08:01 3281834 /lib64/libz.so.1.2.7
7f6191fff000-7f6192000000 rw-p 00017000 08:01 3281834 /lib64/libz.so.1.2.7
7f6192000000-7f6192021000 r-xp 00000000 08:01 3547563 /lib64/ld-2.15.so
7f61921f0000-7f61921f6000 rw-p 00000000 00:00 0
7f619221f000-7f6192221000 rw-p 00000000 00:00 0
7f6192221000-7f6192222000 r--p 00021000 08:01 3547563 /lib64/ld-2.15.so
7f6192222000-7f6192223000 rw-p 00022000 08:01 3547563 /lib64/ld-2.15.so
7f6192223000-7f6192224000 rw-p 00000000 00:00 0
7fff0ade1000-7fff0ae03000 rw-p 00000000 00:00 0 [stack]
7fff0af73000-7fff0af74000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
child killed: SIGABRT
Finished
help?
thanks,
anja
Hi - so the FAST segmentation is failing - maybe you don't have enough SWAP / RAM to complete this? (See the FSL RAM/swap FAW entry).
Have you viewed the input to FAST (brain extracted structural) to check it looks OK?
Cheers.
Hi
I am writing again because I haven't got a reply to my query from 7th October.
I'd appreciate some help this time...
I ran a GLM in which I entered three base regressors (Outcome, Feedback, Choice) and thee regressors modulated by demeaned parametric modulator value (Outcome-mod, Feedback-mod, Choice-mod). With only one subject (out of 20) I am experiencing a problem with
registering example_func to both highres and standard, while registering highres to standard works fine. In particular, I get the following error in the log:
/usr/local/fsl-5/bin/epi_reg: line 311: 19723 Aborted $FSLDIR/bin/fast -o ${vout}_fast ${vrefbrain}
Cannot open volume example_func2highres_fast_pve_2 for reading!
Cannot open volume example_func2highres_fast_wmseg for reading!
/usr/local/fsl-5/bin/epi_reg: line 325: 20093 Aborted $FSLDIR/bin/flirt -ref ${vrefbrain} -in ${vepi} -dof 6 -omat ${vout}_init.mat
Image Exception : #22 :: ERROR: Could not open image example_func2highres_fast_wmseg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-5/bin/epi_reg: line 377: 20160 Aborted $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
Could not open matrix file example_func2highres.mat
/usr/local/fsl-5/bin/epi_reg: line 377: 20161 Segmentation fault $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
Image Exception : #22 :: ERROR: Could not open image example_func2highres
Cannot open sla.png for reading
sh: line 1: 20317 Segmentation fault /usr/local/fsl-5/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png
Cannot open example_func2highres1.png for reading
sh: line 1: 20320 Segmentation fault /usr/local/fsl-5/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png
/bin/rm: cannot remove ‘example_func2highres1.png’: No such file or directory
Could not open matrix file example_func2highres.mat
Cannot read input-matrix
Unrecognised option -
Image Exception : #22 :: ERROR: Could not open image example_func2standard
Cannot open sla.png for reading
sh: line 1: 21206 Segmentation fault /usr/local/fsl-5/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png
Cannot open example_func2standard1.png for reading
sh: line 1: 21211 Segmentation fault /usr/local/fsl-5/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png
Of note, I ran numerous analyses on the same sample of subjects (including parametric modulator with more regressors) and never experienced this problem before. The registration for the remaining 19 subjects works fine.
Your help is greatly appreciated
Thanks very much
Anja
