Hi, Greve,

Thanks a lot! It works. But I got another question now, I used mri_convert to convert a NIFTI file 002.nii to MGZ file 002.mgz. I also want to register 002.nii using the brainmask as the reference volume. Here, 002.nii is a 180x256x256 volume. My command line is

bbregister --s data_2 --mov 002.nii --init-fsl --t1 --reg nureg.dat --o nuDReg.mgz

There is no error when the program is running, however the registration results is bad. Could you give some suggestions?

Guang

Date: Wed, 19 Aug 2009 16:59:11 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkregsiter2 problem

Use bbregister, something like:

bbregister --s subjectname --mov 002.mgz --init-fsl --t1 --reg register.dat --o 002.anat.mgz

Guang Zeng wrote:

...

Hi, there,

I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used as the input of recon-all .... -autorecon1, now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume, which command I can use? tkregister2?

Thanks a lot! Guang

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