Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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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