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