have you tried just putting your original T1 weighted image through the recon stream? You can then sample your T1 maps onto the surface (which we have done in the past). You could plug into our stream after the segmentation, but you would to mirror our directory/file structure, which is going to be somewhat complicated.

Bruce

On Tue, 6 Jun 2006, Nurunisa Neyzi wrote:

Hello,

...

I have whole brain T1 maps and the pseudo T1-weighted images that I created out of them (so they are perfectly aligned). The are all brain extracted using fsl and I am doing my own tissue segmentation (again, using fsl), but in both steps there is much optimization involved, because I want to do it very carefully avoiding partial volume effects (I am looking at the cortical T1 values). I would like to look at the maps in the inflated and flattened spaces. So I have been learning freesurfer over the past week but my problem is with the surface reconstruction and that everything is automated. I don't want freesurfer to do the segmentation for me. I was hoping it would work well because the data is 1x1x1- but the segmentation is not nearly as precise as I need it. Is there a way that I give my already aligned T1 maps and structural images and tissue segmentation and get out the surfaces with T1 values on top of it?