[MINC-users] best_nonlin_reg.pl ?

[Lisa F. Akiyama]

Hi Andrew,

I'm trying to use volgenmodel, but have been running into the following
error:

> Can't exec "volpad": No such file or directory at
> /usr/local/bic/bin/volgenmodel line 656.
> Died at /usr/local/bic/bin/volgenmodel line 656.


I tried finding volpad from http://mavis.anu.edu.au/scripts/ as mentioned on
http://www.bic.mni.mcgill.ca/ServicesHelpDocs/MinctraccError,
but couldn't access it.
Is volpad available elsewhere?

Thanks.


Best,
Lisa

On Tue, Mar 1, 2011 at 11:16 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> 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
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>