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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