[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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