Hello,
I have a problem with bbregister and the option --init-best. In the current dev version of freesurfer 6 the processing stops with the error message:
terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt
if I run bbr using Matlab and the Matlab command 'system', where Matlab was started from a terminal in which all FreeSurfer environment variables are set as described on your webpage. However, if I execute the same bbr command from the terminal in which I started Matlab it seemingly runs without any problems. The output files look okay. There is just one output in the log-file which I do not understand:
(standard_in) 1: illegal character: K (standard_in) 1: syntax error
I got two questions:
1.) Is the run started from the terminal okay? 2.) What do I need to do to get the run started from Matlab to work?
The data used worked fine in the stable version for bbregister with fsl flirt initialization in Matlab. However, --init-best did not work in the stable version. In the example discussed here a single slice was registered to the brain anatomy. Here is some information on my operating system:
lsb_release -a Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core
Can you help me with this issue?
Best Joerg