You have to pass it the name of the subject with the --s flag. The subject name is that produced by recon-all -s subject ...

On 1/4/2025 7:30 AM, Ramesh Babu wrote:

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Hello,

I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local subject space. For this, I want to generate a registration.dat file which will be used for registration with local subject image. But I am facing an issue which I pasted below.

echo $SUBJECTS_DIR
/usr/local/freesurfer/subjects

bbregister --ss sample-001.mgz --mov /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz --reg registration_matrix.dat --init-fsl --dti

ERROR: Flag --ss unrecognized.
--ss sample-001.mgz --mov /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz --reg registration_matrix.dat --init-fsl --dti

I tried with -s flag, but still the same error. Could you please provide me a solution?

Regards

Ramesh

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