[MINC-users] 6-parameter fitting with minctracc

Laurence Mercier laurence at bic.mni.mcgill.ca
Mon Feb 22 15:34:42 EST 2010


Hello again Andrew,

I tried volcombine on 3D ultrasound data.
It gives something that makes sense, but I would probably need to tweek 
the parameters for ultrasound. I get something more blurry then if I 
register them (minctracc -lsq6) and then combine them with minccalc.

Laurence


Laurence Mercier wrote:
> Hello Andrew,
> 
>> 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
> 
> Thank you Andrew! I was just starting to combine 3D ultrasound sweeps 
> (0.3 x 0.3 x 0.3 mm) taken at the same time point during surgery. They 
> mostly overlap, but each of them only covers parts of the region of 
> interest. By combining them I get a much larger field of view. Do you 
> think your script (volcombine) will work for my application? Thank you!
> 
> Laurence
> 
> 
> 
> 
>> 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
> 
> 




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