Hi Guang,

to register two volumes of the same person (6 degree of freedom: translation, rotation) you can use mri_robust_register --mov 002.mgz --dst 001.mgz --lta 2to1.lta --warp 2to1.mgz

This will register 002.mgz to 001.mgz output the transform 2to1.lta and the source mapped to the target as 2to1.mgz. Note that 2to1.mgz is interpolated so will be more blurry than the originals 001.mgz or 002.mgz.

I would recommend to additionally use the --iscale flag. This will allow intensity scaling (as a 7th parameter). It is useful if the images are not normalized and leads to better registrations. More Infos here: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register

I do not understand, what you mean with "using brainmask.mgz as reference volume"? Of course it is always better to register only brain instead of full head images, however for 002.mgz you only have the full head image. If you want to use the brainmask, do this: 1. register 002 to 001 as described above (using full head) 2. do a more accurate registration by masking each volume with the brainmask (you need to check if 002 looks ok after masking). For the second registration you can input the 2to1.lta as initial transform with --transform 2to1.lta

Also, I don't know your setup or goal, but if you are trying to do a longitudinal study with two timepoints, have a look at the Freesurfer longitudinal stream http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

Hope that help,

Cheers, Martin

On Thu, 2009-08-20 at 10:08 -0500, Guang Zeng wrote:

Hi, there,

Sorry, I asked the same question yesterday, but I think I didn't explain it clear. 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, and I only run -autorecon1. now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume.

Dr. Greve mentioned that I can use bbregister, but I got a problem now, becuase I only run autorecon1, I do not have lh.white which will be acquired after autorecon2. The bbregister command stopped in the middel.

My command line is

bbregister --s data_2 --mov 002.mgz --init-fsl --t1 --reg brainreg.dat --o brainmaskReg.mgz

I got a error as,

Loading mov Loading lh.white surf No such file or directory

Is there an option that I do not use lh.white, just use the information I got after autorecon1 to do the registration, or I need use other commands?

Thanks a lot!

Guang

---

Windows Live: Make it easier for your friends to see what you’re up to on Facebook. Find out more. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer