Hi Longchuan

have you tried the -cm (conform to min) option in recon-all?

cheers
Bruce


On Sun, 18 Nov
2012, Longchuan Li wrote:

> Hi, FreeSurfer experts
>
> I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I
> am working on non-human primates and noticed that my white and pial surfaces do not have identical positions as brain.mgz. For
> example, when I used "mris_fill" to write white and pial surfaces into volume files, they do not have same sto_xyz and qto_xyz
> values as these in the brain.mgz. This is not the case for human data. So my questions are:
>
> (1) how could I find a transformation matrix between the two, so that when I am using surface-based tractography in the future,
> the program can find the correspondence between the points on the surfaces and those in the volumetric diffusion MRI data? 
>
> (2) How in the future, can I avoid such misregistrations in generating non-human primate surface files in FreeSurfer? 
>
> Thank you very much in advance!
>
> Longchuan
>
>


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