Hi Longchuan, mris_fill create a volume with a different geometry than orig.mgz (though it is in the same space). What do you want to do exactly? Map the output of mris_fill into the DTI space? The transform from the output of mris_fill to orig.mgz is easy to obtain:
tkregister2 --noedit --mov mris_fill.mgz --s subject --regheader --reg mris_fill.reg.dat
this will be in "register.dat" format/space.
doug
On 11/19/2012 03:35 PM, Longchuan Li wrote:
Hi, Doug
I tried bbregister and checked the registration using tkregister2. It seems that this program registers the diffusion image with the anatomical *volume* images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am working on monkey data and I found that my ?h.white surfaces do not have the identical sto_xyz coordinates as those of the anatomical volume images, such as brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a volume file, I find that the center of the images in the header file is not identical to that of the anatomical volume images. In my human data processed using FreeSurfer standard recon-all pipeline, they are identical. Since I am working on monkey data, I used "-notalairach" and "-notal-check" in recon-all to have the piepline work. I suspect this may be related to these options.
So my questions are: (1) what do you think are the reasons causing the inconsistent sto_xyz values between the surface files (?h.white) and voluem files in the non-human data.
(2) Is there any way that I could find a transformation matrix between the ?h.white and my FreeSurfer volume images (such as brain.mgz)?
thank you!
Longchuan
PS: I also used "-cm" option in recon-all as suggested by Bruce. I just got the results and the problem is still there.
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, November 19, 2012 10:43 AM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
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
mailto:fischl@nmr.mgh.harvard.edu>
To: Longchuan Li <leonado78@yahoo.com mailto:leonado78@yahoo.com> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto: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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