Re: [Freesurfer] recon-all error

[Smian]

Thank you for your reponse. The registration has turned out quite 
strangely (please see attached). I checked the first value in the 
mincost file and it is quite high (~0.95). I'm assuming that means that 
the initialization was bad. I tried changing the initialization from fsl 
to spm and header, but that failed too. Would you know why this could be 
occurring and how I might be able to fix it?

Thank you!

On 2013-07-23 16:07, Bruce Fischl wrote:
you can use bbregister to register your T2* volumes to the surface, 
then
mri_vol2surf to sample and display it.

cheers
Bruce
On Tue, 23 Jul 2013, Smian wrote:

Hi everyone,

To put things into context, I am trying to follow the four step
methodology outlined in this paper (Cohen-Adad, 2013)
http://www.sciencedirect.com/science/article/pii/S1053811913000700

I have already performed recon-all on MPRAGE data. I have also carried
out the following steps:

1) Reconstruct cortical surface
2) Register T1 to the surface
3) Sample T1 at a given cortical depth
4) Register surface to fsaverage

I have now been told to use the T2* information from the fourth echo 
of
separately acquired T2* weighted data and to 'overlay' (I'm not sure 
if
this is the correct usage of this technical term) it on the surfaces
produced (as above) of the MPRAGE data. I realize that I can't perform
recon-all on this T2* weighted data. I am assuming that I need to 
carry
out steps similar to 1)-4) on this new data, but I'm not sure. Would 
you
have any guidance on how to go about this?

Any help would be appreciated!

Thank you!

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