Dear Erick,

The limitations to the resolution obtainable with the current version  
of fnirt is not so much execution time as it is memory demands. I  
think realistically that you cannot obtain a higher warp resolution  
than 5mm, and even then you will need a powerful computer with a lot  
of memory.

That does not mean you cannot register your images to a template with  
higher resolution than that. You can use the warp fields you obtain  
from the "standard" fnirt registration to resample your images into  
MNI 1mm or 0.5mm space by specifying one of those as the --ref  
argument to applywarp. It should also be noted that a warp resolution  
(knot spacing) of 10mm (the standard) does not imply a 10mm  
registration error. My guesstimate is that registration errors in the  
cortex are in the range 2-5mm, and less for central structures.

The next version of fnirt will have the ability use a warp resolution  
down to 1mm with reasonable memory requirements. When testing this  
version I have found marginal advantages with 1mm over and above 10mm  
for normal healthy subjects. The big difference, and benefit, is  
mainly evident for elderly atrophied brains.

Jesper

On 13 Dec 2010, at 10:21, Erick Canales Rodriguez (Benito Menni CASM)  
wrote:

> Dear FSL experts,
>
> By default FNIRT was designed to be a "medium resolution” method  
> that provides an excellent tradeoff between the accuracy of the non- 
> linear registration and execution time (and working memory).
> However, my main interest is to apply the non-linear registration as  
> accurate as possible – the execution time per subject is not a  
> problem for my application. I am willing to wait as long as needed  
> (within an interval of 24 hours) in order to obtain the most  
> accurate result.
>
> This particular mode of operation is not aimed to be used in  
> standard methods like VBM. In my project I need to obtain accurate  
> high resolution “displacement field”, which will be used to  
> transforms particular points from the native space to the MNI space  
> (for example, the points belonging to a particular tract {xi,yi,zi,  
> i=1..n} reconstructed by DTI and deterministic tractography  
> algorithms).
> There are any “optimal” configuration files to perform this type of  
> high resolution registration from the native space to the templates  
> MNI152_T1_1mm or MNI152_T1_0.5mm?
>
> Any recommendations would be appreciated,
>
> Many thanks,
>
> Erick J. Canales-Rodríguez
>
> (+34) 93 652 99 99 ext. 255
> Unitat de Recerca, Benito Menni CASM
> Sant Boi del Llobregat (Barcelona), Spain
>
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