[MINC-users] best_nonlin_reg.pl ?

[Lisa F. Akiyama]

Hi Andrew,

Thank you once again - I am always surprised (in a good way, of course) and
thankful for how supportive people, like you, are on this MINC mailing list!

Thanks for suggesting me "volgenmodel".
Yes, by reading his paper, I realized that Vladimir used other codes like
ITK in his model creation process.
Seems like volgemodel will be a great start off for this project. I will
definitely try out volgenmodel.

The difference as he mentions in his paper is that he doesn't start
> fitting from scratch at each step. volgenmodel does but there are
> other reasons for this.


What are some of the reasons for this?

Thank you.


Best,
Lisa

On Mon, Feb 28, 2011 at 9:35 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi again Lisa,
>
> > I am trying to create average infant head templates similar to what Fonov
> et
> > al 2011 have created with the pediatric population.
> > (He informed me that the infant templates available online were created
> > using similar methods as stated in his 2011 paper involving pediatric
> data)
>
> > Thanks for guiding me on how to modify the configurations.
> > As a start, I will play around with nlpfit and fit config (I'll use what
> > Fonov et al used for their settings as a guidance).
>
> OK, now I am with you. Vladimir (Fonov) wrote a ruby? script that
> behaves much as 'volgenmodel'
> (http://packages.bic.mni.mcgill.ca/scripts/volgenmodel)  does. The
> difference as he mentions in his paper is that he doesn't start
> fitting from scratch at each step. volgenmodel does but there are
> other reasons for this.
>
> You are welcome to use it as a start if only because last I looked at
> Vladimir's scripts they use a lot of his own mashups of others code
> (mincANTS, ITK etc). In time you should be able to get his version
> working but I suspect volgenmodel will make a good starting step.
>
> It has a few dependencies on other scripts that I have also uploaded
> to the scripts directory, note that a run of this script will take a
> LONG time if you dont run it on a batch (SGE/gridengine) setup.  For
> example a run on 200 elderly brains takes approximately 1 week on a
> 50core linux cluster.
>
> Usage is like this:
>
>   $ volgenmodel -check -clean -symmetric -normalise -extend 5 \
>      -output_model <model.mnc> -workdir genmodel-work \
>      <infiles>
>
> The -check option generated JPG files in the workdir, -clean removes a
> bunch of working files as it goes along, -symmetric makes a symmetric
> model, -normalise takes care of global intensity differences between
> images, -extend 5 adds a 5 voxel boundary around all the images in
> case the cropping/framing is off.
>
> Note that for 100 subjects this will need about 700GB of spare space
> in the -workdir directory if the -clean option isn't used.
>
> Good luck.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Brisbane->Australia    +61 (402) 700 883
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