Hi, I'm afraid I don't know what might be causing this error. Can you upload the data to: https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C Hopefully we can figure out what is going wrong when we see the data. All the best, Mark On 11 Oct 2013, at 12:49, Andreja Varjacic <[log in to unmask]<mailto:[log in to unmask]>> wrote: 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 ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Stephen Smith [[log in to unmask]<mailto:[log in to unmask]>] Sent: 11 October 2013 10:45 To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] Registration problem for one subject 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. On 11 Oct 2013, at 10:36, Anja <[log in to unmask]<mailto:[log in to unmask]>> wrote: 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 --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net>