[MINC-users] 6-parameter fitting with minctracc

[EJ Nikelski]

Hi all,

   Thanks Andrew, I shall try your magic and report back to the list
for completeness ... although the reason for non-linear fitting still
confuses and angers me ...

-Jim


On Sat, Feb 20, 2010 at 9:54 PM, Andrew Janke <a.janke at gmail.com> wrote:
> 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University