Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to
see if the problem will be solved. In the mean time, do you have any
suggestions regarding finding a transformation between the mismatched surfaces
and the volume?
Thanks again.
Longchuan
________________________________
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
To: Longchuan Li <leonad...@yahoo.com>
Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, November 19, 2012 8:57 AM
Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
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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