[MINC-users] nonlinear registration in minc

[Ernest Lo]

Hello,

Thank you all very much for your advice and help (including any pending
suggestions as well :).  I am in the process of assimilating all the
information and trying out the different methods.


Ernest Lo
NeuroRX Research
Montreal, Canada


> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 2 Mar 2006 07:14:27 +1000
> From: "Andrew Janke" <a.janke at gmail.com>
> Subject: Re: [MINC-users] nonlinear registration in minc
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> 	<d747ed50603011314p791cc011p1c5d8d1cb55e7cda at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> > >I would like to perform a nonlinear registration of one image to another.
> > >In fact it is the same patient, but there is some minor distortion in one
> > >of the scans (that is affecting our tissue segmentation results).  So I'm
> > >looking for a registration technique that will not only align the images
> > >but correct for the distortion.
> 
> > There are, as far as I know, no convenient scripts available for subject
> > to subject non-linear registration. So you'll have to use minctracc
> > itself. The basic options you want are:
> >
> > -nonlinear: erm, I'm sure you can figure out what this option does.
> > -xcorr: objective function
> > -step: 3 values for the spacing of the deformation grid.
> > -simplex: size of search area.
> > -lattice_diameter: width of sub-lattice (three values)
> > -iterations: number of iterations.
> 
> Hi Ernest,
> 
> Jason is right, there is no officially blessed script for doing this,
> but of course I do have one myself that you are welcome to use.  You
> may have to modify the first part (config) of the script for your
> application but it generally does a good job as is. This script does
> all the required blurring and hierarchical fitting that you will need.
> 
> I have attached it.
> 
> 
> 
> --
> Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 01 Mar 2006 16:40:24 -0500
> From: Andre Matos <amatos at mrs.mni.mcgill.ca>
> Subject: Re: [MINC-users] nonlinear registration in minc
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID: <C02B7EF8.199E7%amatos at mrs.mni.mcgill.ca>
> Content-Type: text/plain;	charset="US-ASCII"
> 
> Hi Ernest,
> 
> Did you speak with Sridar or Louis Collins regarding this? We have some
> nonlinear transformations done in the lab and Patricia (from Louis lab) did
> for us.
> 
> Andre
> 
> 
> On 3/1/06 9:26 AM, "Ernest Lo" <elo at neurorx.com> wrote:
> 
> > Hello,
> > 
> > I would like to perform a nonlinear registration of one image to another.
> > In fact it is the same patient, but there is some minor distortion in one
> > of the scans (that is affecting our tissue segmentation results).  So I'm
> > looking for a registration technique that will not only align the images
> > but correct for the distortion.
> > 
> > I have experimented with minctracc -nonlinear and mritoself with no
> > success.  I don't have much experience in this area but it seems to me
> > that a good nonlinear reg algorithm should be able to easily align these
> > two images.  Would anyone know of a good way to do this, in terms of
> > parameter settings, scripts, commands, etc.?
> > 
> > I have access to a couple of tools as well - nlfit_xcorr.pl and
> > nlfit_smr.pl - but these require various model files in addition to the
> > target image (blur levels etc.), which I don't know how to generate.  Any
> > advice in this area would be appreciated as well.
> > 
> > Thanks!
> > 
> > 
> > Ernest Lo
> > NeuroRX Research
> > Montreal, Canada
> > 
> > 
> > 
> > 
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> 
>