Getting errors on a fresh install of 3.0.3 Tiger release. Any suggestions appreciated. If any more info is needed/would help just let me know.
Command:
mri_convert <input> <output>
Error:
dyld: mri_convert Undefined symbols: mri_convert undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib mri_convert undefined reference to ___stdoutp expected to be defined in /usr/lib/libSystem.B.dylib Trace/BPT trap
(Error is reproducible using any Freesurfer utility as far as I can tell)
Current working environment var $DYLD_LIBRARY_PATH :
echo $DYLD_LIBRARY_PATH $FREESURFER_HOME/lib/misc/lib:$FREESURFER_HOME/lib/tcltktixblt/lib: $FREESURFER_HOME/lib/gsl/lib:$FREESURFER_HOME/freesurfer/lib/
(replaced absolute path with the $FREESURFER_HOME var.)
GDB backtrace output:
run subjects/bert/mri/T1.mgz test.img Starting program: $FREESURFER_HOME/bin/mri_convert subjects/bert/mri/ T1.mgz test.img Reading symbols for shared libraries ++.. done dyld: $FREESURFER_HOME/bin/mri_convert Undefined symbols: $FREESURFER_HOME/bin/mri_convert undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib $FREESURFER_HOME/bin/mri_convert undefined reference to ___stdoutp expected to be defined in /usr/lib/libSystem.B.dylib Program received signal SIGTRAP, Trace/breakpoint trap. 0x8fe01400 in __dyld_halt () (gdb) backtrace full #0 0x8fe01400 in __dyld_halt () No symbol table info available. #1 0x8fe0a2b0 in __dyld_check_and_report_undefineds () No symbol table info available. #2 0x8fe113b0 in __dyld_link_in_need_modules () No symbol table info available. #3 0x8fe0166c in __dyld__dyld_init () No symbol table info available.
Are you certain you are running the Tiger release of Mac OS/X, aka v10.4.#? I have seen these errors when running the Tiger freesurfer release on Panther (aka v10.3.9).
Click the 'About this Mac' menu item on the blue apple icon to see which Mac OS/X version is running. If using 10.3.9, then there is a freesurfer installation for Panther. v10.4.7 is the most current Mac OS/X release.
On Wed, 2006-07-19 at 13:46 -0700, James Kyle wrote:
Getting errors on a fresh install of 3.0.3 Tiger release. Any suggestions appreciated. If any more info is needed/would help just let me know.
Command:
mri_convert <input> <output>
Error:
dyld: mri_convert Undefined symbols: mri_convert undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib mri_convert undefined reference to ___stdoutp expected to be defined in /usr/lib/libSystem.B.dylib Trace/BPT trap
(Error is reproducible using any Freesurfer utility as far as I can tell)
Current working environment var $DYLD_LIBRARY_PATH :
echo $DYLD_LIBRARY_PATH $FREESURFER_HOME/lib/misc/lib:$FREESURFER_HOME/lib/tcltktixblt/lib: $FREESURFER_HOME/lib/gsl/lib:$FREESURFER_HOME/freesurfer/lib/
(replaced absolute path with the $FREESURFER_HOME var.)
GDB backtrace output:
run subjects/bert/mri/T1.mgz test.img Starting program: $FREESURFER_HOME/bin/mri_convert subjects/bert/mri/ T1.mgz test.img Reading symbols for shared libraries ++.. done dyld: $FREESURFER_HOME/bin/mri_convert Undefined symbols: $FREESURFER_HOME/bin/mri_convert undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib $FREESURFER_HOME/bin/mri_convert undefined reference to ___stdoutp expected to be defined in /usr/lib/libSystem.B.dylib Program received signal SIGTRAP, Trace/breakpoint trap. 0x8fe01400 in __dyld_halt () (gdb) backtrace full #0 0x8fe01400 in __dyld_halt () No symbol table info available. #1 0x8fe0a2b0 in __dyld_check_and_report_undefineds () No symbol table info available. #2 0x8fe113b0 in __dyld_link_in_need_modules () No symbol table info available. #3 0x8fe0166c in __dyld__dyld_init () No symbol table info available. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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James Kyle -
Nick Schmansky