Hi,
I managed to get this to work at this end, so it
is not a "bad" image. Note that the bet result is
poor though, and you would do a lot better if you
set the centre using the -c option (this is necessary
because of the large amount of neck in the image).
I used -c 119 93 137 and it was a lot better.
Anyway, we have known that flirt can crash on redhat
related systems, and released a patch several months
ago. Is you distribution patched?
If not, then download the appropriate patch from
http://www.fmrib.ox.ac.uk/fsldownloads/patches/3.2/
If so, then it might be necessary to compile a version
with the compiler installed on your system. We can
help with that if you have trouble.
Let us know how you get on.
All the best,
Mark
Donna Hanlon wrote:
> Hi all,
>
> First, I'd like to take this opportunity to thank you for making such
> useful tools freely available.
>
> Now, for my problem -- I have spatially normalized 60 volumes like so:
>
> bet 1421 1421_bet -f 0.5 -g 0
> flirt -in avg152T1_brain_lpi -ref 1421_bet -omat avg152_to_1421 -bins
> 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90
> -dof 12 -interp trilinear
> [steps for inverting matrix and applying to volume snipped]
>
> For the two volumes in this gzipped tar archive, however, flirt core
> dumps during the flirt step:
>
> http://pub:[log in to unmask]
>
> login pub
> password download
>
> The avg152T1_brain_lpi also is included and is just a x-flipped
> version of fsl/etc/standard/avg152T1_brain.hdr.
>
> Here is output from gdb, if it proves helpful:
>
> GNU gdb Red Hat Linux (6.3.0.0-0.30.1rh)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and
> you are
> welcome to change it and/or distribute copies of it under certain
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for
> details.
> This GDB was configured as "i386-redhat-linux-gnu"...Using host
> libthread_db library "/lib/tls/libthread_db.so.1".
>
> Core was generated by `flirt -in avg152T1_brain_lpi -ref 1421_bet
> -omat avg152_to_1421 -bins 256 -cost'.
> Program terminated with signal 11, Segmentation fault.
> Reading symbols from /usr/lib/libstdc++-libc6.2-2.so.3...done.
> Loaded symbols for /usr/lib/libstdc++-libc6.2-2.so.3
> Reading symbols from /lib/tls/libm.so.6...done.
> Loaded symbols for /lib/tls/libm.so.6
> Reading symbols from /lib/tls/libc.so.6...done.
> Loaded symbols for /lib/tls/libc.so.6
> Reading symbols from /lib/libgcc_s.so.1...done.
> Loaded symbols for /lib/libgcc_s.so.1
> Reading symbols from /lib/ld-linux.so.2...done.
> Loaded symbols for /lib/ld-linux.so.2
> #0 0x082c4bfd in NEWIMAGE::p_corr_ratio_smoothed ()
> (gdb) where
> #0 0x082c4bfd in NEWIMAGE::p_corr_ratio_smoothed ()
> #1 0x082cfe8c in NEWIMAGE::Costfn::corr_ratio_smoothed ()
> #2 0x082c30ac in NEWIMAGE::Costfn::cost ()
> #3 0x08093642 in costfn ()
> #4 0x08096091 in costfn ()
> #5 0x082dc3b9 in MISCMATHS::optimise1d ()
> #6 0x082dc860 in MISCMATHS::optimise ()
> #7 0x0808ec08 in optimise ()
> #8 0x081468bc in optimise_strategy1 ()
> #9 0x081bd0eb in usroptimise ()
> #10 0x081ddbb2 in interpretcommand ()
> #11 0x08208b19 in main ()
> (gdb) quit
>
> I'm running Red Hat Enterprise Linux AS release 3 (Taroon Update 5),
> 2.4.21-32.0.1.ELsmp, on a Dell Precision 450n.
>
> Any ideas for what I might try? This looks like it might be similar
> to this problem:
>
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0505&L=FSL&P=R14178&I=-3
>
> Thanks much,
>
> Donna Hanlon
> Van Essen Lab
