Thank you. Now I understand the last changes to this functionality. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, April 24, 2019 9:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: flirt in bbr Matlab Execution

Don't use --best anymore, it is depricated. There should be no need to specify an initialization (unless it is to initialize it with the header geometry). Under the hood, it will use mri_coreg (a shameless copy of spmreg).

On 4/24/2019 7:07 PM, Pfannmoeller, Joerg Peter wrote: 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

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what version of FSL are you running? That program (mni152reg) is just a front end for running flirt, so you can always run flirt by itself.

On 5/13/2019 8:49 AM, vin rasa wrote:

External Email - Use Caution

Dear Freesurfer Experts!

The idea is to transform freesurfer output in to the MNI 1mm space using following command:

mni152reg --s subject_id --1

But mni152reg crashes with following error:

flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' ERROR: flirt

Your help is appreciated!

Thank you

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