Well, it gives out an error that the file given for srcreg is unkown or cannot be found. So mainly I think the problem is that I defined the "wrong" file there.

I run bbregister with the following command:

bbregister --s subid --mov mcT2_MAP.nii.gz --init-rr --reg T2.reg --t2 --o /path/to/my/output

I also tried to use T2.reg, but I didn't work: "ERROR: Option T2.reg is unknown"

Gesendet: Mittwoch, 17. November 2021 um 16:11 Uhr
Von: "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Using Mri_vol2surf

Can you be more specific about why it is not working? You definitely need to run bbregister to create a registration file

On 11/17/2021 7:09 AM, m-maiworm@web.de wrote:

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Dear List,

I first run the recon-all stream using a MPRAGE as input, then bbregister to move other mri-sequences to this MPRAGE. Now I want to transfer the values from these mri-sequences to the surface, so that I can calculate on the surface and perform a group analysis.

I tried different input files, but it doesn't work...

my command is

mri_vol2surf --src /path/to/my/subject --out /path/to/my/output --srcreg ???? --surfreg --hemi ?h --fwmh 1,5

I wonder wheather I need an extra step to perform the registration file? Because in my current freesurfer output I can't find an "registration.dat"...

Moreover I want to create thalamus/basalganglia/ventricle/amygdala etc masks, and I don't know how to automate this - does anybody know if there exists a command?

Thanks for your help!

Best, M
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