If you already have run freesurfer on one of the time points, you can use bbregister to do the registration, then mri_vol2vol to apply it (or use mri_label2vol for the mask).

doug

On 8/11/10 11:56 PM, Mehul Sampat wrote:

Hi Folks,

I have two MR scans per subject.
Lesions (white matter hypo-intensities) have been manually outlined for the first time-point.

I would like to create a lesion mask for the 2nd time-point.
But instead of starting from scratch, I would like to use the lesion-mask from the 1st time-point as a starting point for the lesion mask for time-point 2.

for this task, I think I can use the following steps:

Step 1) Register 1st time-point to the 2nd scan (using 2nd timepoint as reference) with flirt
Step 2) Use mri_convert to apply the transformation matrix from flirt to the lesion mask and create a lesion mask for time-point 2.
Step 3) make corrections to the lesion mask for time-point 2 if required.

Would you suggest to do it in this manner or is an alternative approach recommended ?
thanks
Mehul
ps: I thought of using the longitudinal freesurfer pipeline but i dont know how to compute the transformation matrix from time-point 1 to time-point 2 use the pipeline...
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