Chacko,
The -long flag, supporting longitudinal analysis, has not yet been released in the public stable enviro. The recon-all script you are using is intended for the the non-public 'dev' environment, which contains some options not yet released. One such is the -topofix flag to mri_fill.
The solution is to either edit your recon-all script and remove the line where it adds '-topofix norm.mgz' to the command string, or add the '- use-old-fixer' flag to recon-all, which will exclude usage of the '- topofix' flag.
Nick
On Wed, 2007-03-07 at 10:14 -0800, Chacko Cherian wrote:
Hello all,
I got an error while running longitudinal analysis using recon-all -long and the process exited with errors. THis is the error message:
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... fill: could not scan threshold from 'norm.mgz'Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux
recon-all-long exited with ERRORS at Tue Feb 13 20:59:04 MST 2007
Could someone give me suggestions on what could have gone wrong..thanks in advance.
Regards
Chacko.
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