Hi, Doug

Thank you very much for the information. What I want to do is to use the white and pial surfaces in the FreeSurfer space as the seeds for surface-based tractography implemented in FSL. In order to do that, I need a transformation between the white matter surface and diffusion MR data. For some reason, the space of the white matter surface in my monkey data is not the same as that of the other volumetric data, such as filled.mgz, orig.mgz. This is however not the case for humans, which are processed using the standard FreeSurfer pipeline.  

To make things worse, I used "cm" option in recon-all and processed the data in their original resolution(0.5mm isotropic). When I used "mris_fill" without "-c" option, the left and right white volumes will have different dimensions, making it difficult to combine them for registering with filled.mgz. If I use "-c" option, I can combine them since they now have the same dimension. However, they would be "conformed" to 1mm isotropic (originally 0.5m isotropic), which is severely downsampled. I am afraid that this downsampling from 0.5mm to 1mm will affect the registration results. Do you have any suggestions on solving the issue?

I am planning to change the resolution of the image from 0.5mm to 1mm without downsampling before I feed the image to recon-all. I noticed that there are two options in mri_convert (-vs, -cs) that are supposed to be related to this. However, I found both of them downsample the images. Is there any way that I could change the resolution of the images from 0.5mm to 1mm and in the mean time, magnifying the images so that the partial volume effect of the image will not change?

Thank you !

Longchuan

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Longchuan Li <leonado78@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>; Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Tuesday, November 20, 2012 3:19 PM
Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz


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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> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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>

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/