Hi Sarah,
the ex vivo analysis stream is kind of a work in progress. If the brain has been fixed it removes almost all the T1 contrast and pretty much all that remains is T2*. What was your TE? For that TR I would try a longish TE, probably around 15 or 20 ms, and minimize your bandwidth.
cheers Bruce
On Mon, 31 Jan 2011, Sarah Whittle wrote:
Hi,
I have some post-mortem MR images that I'd like to run through FreeSurfer to obtain thickness estimates. I've had a look at the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo. The images were obtained with a T1-weighted fast gradient echo sequence (1.5-mm slice thickness, FOV = 25 cm; NEX = 1; matrix = 256 x 192; TR = 35 ms; FA = 60). Although the images are T1-weighted, they appear to look like T2-weighted images (ie, dark WM, white GM). I haven't worked with post-mortem MRI before, and my knowledge of MR physics isn't great, so I'm not sure why that is.
So, my questions are, 1) can I use these images in the processing stream described on the wiki? 2) Is it possible to do the automated atlas-based cortical and subcortical parcellations?
Thanks,
Sarah