Hi Mehul,
- if lesions show large changes, normalization might be dangerous - mri_robust_register has a flag --iscale for global intensity adjustment (a global scaling parameter that adjusts the intensity images of both inputs to better match) - mri_normalize, normalized the white matter to be around 110 is that what you want? - usually registration will be more accurate if images are skull stripped.
Best, Martin
On Tue, 2012-01-24 at 09:39 -0800, Mehul Sampat wrote:
Hi Folks, We have subjects with high lesion load which changes significantly over time. I want to use FS functions to build a pipeline for comparing lesion changes in two time-points of the same-subject. I am thinking of using the following steps;
- Use mri_normalize to normalize the two time-points.
- Use mri_robust_register to register two time-points of the same
subject to half-way space. 3) Use mri_skull_strip 4) Use subtraction imaging or some other techniques to look for lesion changes.
My questions are:
- I think I need mri_normalize since the output from
mri_robust_register is not intensity normalized ? 2) Instead of the first three steps, I could also do the following: Run autorecon1 for both timepoints and then run mri_robust_register on the skull stripped images Does it matter if we run mri_robust_register before or after skull stripping ?
Thanks Mehul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer