Hi, Bruce and Doug
Thank you very much for the information. I will try this command to register
the surfaces with my diffusion volumetric data.
Best
Longchuan
________________________________
From: Douglas N Greve <gr...@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 <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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>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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