what version of freesurfer are you running?

On Mon, 2010-01-25 at 10:12 -0600, Guang Zeng wrote:

Hi, there,

I have some scans which have poor white matter and gray matter contrast, and the results of the intensity normalization step are pretty bad. So I add some controls, the results looks much better now.

But I met a question now, I sent these results-improved subjects to FS longitudinal stream without those controls points, the longitudinal results are as bad as before.

My command line is: recon-all -base subj_based_id -tp subj1 -tp subj2 -all recon-all -long subj1 subj_base -all recon-all -long subj2 subj_base -all

I think the problem is the FS surfer longitudinal stream will copy the orig.mgz of each time point, map them to the base template, and then go through FS stream again. How can I map my added control points to the base template, and use them in the longitudinal stream, or I should map it to somewhere at the recon-all -base subj_based_id -tp subj1 -tp subj2 -all step.

Thanks!

Guang

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