[MINC-users] 6-parameter fitting with minctracc

Andrew Janke a.janke at gmail.com
Sun Feb 21 00:54:11 EST 2010


Hi Jim,

On Sun, Feb 21, 2010 at 06:13, Vladimir Fonov <vladimir.fonov at gmail.com> wrote:
> I also suggest using nonlinear registration ( 8mm step size should be
> enough) or at least lsq12 when averaging scans acquired during
> different scanning sessions. Also, do you normalize intensities
> between scans ?

And to follow on from others comments one of the more interesting
points you should consider is that you should be resampling all your
files equally (or transforming them as much as all the others) in
order than you don't bias your result to one image.  I am being
pedantic I know but it's fun.

So to this end I wrote a thing called volcombine for just this reason
(joining up 2 T1's).. :)  It generates a fit mask as part of the
process as often subjects tend to move their faces and the likes.  It
makes sure the result is 1/2 between the two input images. Get it
here:

   http://mavis.anu.edu.au/scripts/volcombine

mavis:~$ volcombine -help
Usage:
    volcombine [options] <in1.mnc> <in2mnc> <outfile.mnc>

    volcombine uses linear registration to combine two volumes into one.
    These volumes are typically from a dual-acquisition that is used to
    improve SNR and/or reduce movement artifact

       $ volcombine T1-1.mnc T1-2.mnc outfile.mnc

If you have more than 2 files then you could always use volgenmodel from here:

   http://mavis.anu.edu.au/scripts/volgenmodel

I would run it with this magic incantation:

   $ volgenmodel in1.mnc in2.mnc in3.mnc ... \
         -output_model all-together-now.mnc \
         -fit_stages lin,lin,lin,0,0,0,1,1,1

This will do 3 linear fits and then 3 nonlinear fits at the 16mm
level.  You can change the fit parameters if you want with
-config_file. Also if you have a SGE batch system and qbatch you can
add a -batch option and it will suck up all the CPU's it can find.

With both of these there may be a few other scripts that you will have
to download from the same directory..

Good luck!


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


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