Hi, Doug
Thank you for following up the issue. I think that I have solved the problem.
What I wanted was to derive a binary map of the surface in the DTI space so
that each cortex voxel can be used as a seed.
Thank you very much for the help!
Longchuan
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Longchuan Li <leonad...@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, November 21, 2012 3:20 PM
Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan, I'm still not sure I understand what you are trying to do
ultimately. Do you just want a binary map of the surface in the DTI
space so that you can use each cortex voxel as a seed? Or do you want to
use one of the surface-based ROIs as the seed? This should be possible
without re-running recon-all at 1mm.
doug
On 11/20/2012 06:01 PM, Longchuan Li wrote:
> 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 <gr...@nmr.mgh.harvard.edu>
> *To:* Longchuan Li <leonad...@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu"
> <freesurfer@nmr.mgh.harvard.edu>; Bruce Fischl
> <fis...@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 <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> <mailto: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
> <mailto:fis...@nmr.mgh.harvard.edu> <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>>>
> > >> To: Longchuan Li <leonad...@yahoo.com
> <mailto:leonad...@yahoo.com> <mailto:leonad...@yahoo.com
> <mailto:leonad...@yahoo.com>>>
> > >> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> <mailto: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
> > >> >
> > >> >
> > >>
> > >>
> > >> 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
> > >> dispose of the e-mail.
> > >>
> > >>
> > >>
> > >>
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > -- Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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/
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@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/
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/
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