Hi,
I'm having problems with run_first. I first tried run_first_all with not much success so decided on doing the registrations separately first. These worked out and now I'm trying to perform a segmentation. I'm trying to get the hippocampi.
I encounter the following error:
create shapeModel
done creating shapeModel
/usr/local/fsl/bin/run_first: line 164: 37686 Abort trap ${FSLDIR}/bin/first -i $image -l $trmat -m $model -k $outname -n $modes $verbose $comExtras
I have no idea what Abort trap could refer to and google so far hasn't helped. The algorithm doesn't output anything, not even some logs or whatever to see why it's crashing. This is how I run the command:
run_first -i myfile.nii.gz -t myfile_to_std_sub.mat -n 50 -o output_name_L_Hipp -m /usr/local/fsl/data/first/models_336_bin/L_Hipp_bin.bmv
This is how the documentation, if I understood it correctly, requires you to do it. Any ideas what is going on here?? How can I solve this?? Any help will be greatly appreciated!
P.S. I'm running FSL 5.0.1 on a Mac 10.6. I'm pretty sure everything is installed properly and all the pathnames etc to the libraries are correct.
