[Mrtrix-discussion] output file of "find_SH_peaks"

[Kerstin Pannek]

Thanks Donald. I meant spatial resolution.

Cheers
Kerstin



On 16/02/2011, at 5:04 PM, Donald Tournier wrote:

> Hi Kerstin,
> 
> Not sure what you mean by 'higher resolution'. Do you mean spatial resolution? If so all you'd need to do is to interpolate the CSD image to a higher resolution prior to feeding it into find_SH_peaks. I think mrtransform might do the trick if you give it a higher resolution anatomical image (for example) as the template image.
> 
> If you meant angular resolution, then I should point out that the find_SH_peaks command does a full Newton-Raphson type gradient ascent, and finds the exact peak direction. The direction set that you need to provide to the command simply specifies a set of initial directions from which to start the search. So basically find_SH_peaks already provides 'full' angular resolution.
> 
> Cheers,
> 
> Donald.
> 
> 
> On 16 February 2011 12:58, Kerstin Pannek <uqkpann1 at uq.edu.au> wrote:
> Hi
> 
> is it possible to get the peaks at a higher resolution than the input csd?
> 
> Cheers
> Kerstin
> 
> 
> 
> On 15/02/2011, at 9:42 AM, Donald Tournier wrote:
> 
>> Hi Jeong,
>> 
>> I wonder the order of fiber directions saved in the output file of "find_SH_peaks".
>> 
>> This is what I did:
>> 
>> gendir 100 dir100.txt
>> 
>> find_SH_peak CSD8.mif dir100.txt SH_peaks_CSD8.mif
>> 
>>  
>> The output file consists of 9 different 3-D volumes.
>> 
>> Which ones are for X, Y, Z to indicate the direction of the 1st fiber ?
>> 
>> I am guessing the first three volumes indicates the X, Y, Z of the first vector, next three indicates those of the second vector, and so on.
>> 
>> Is it correct?
>> 
>> 
>> Yes, this is correct. Also, the norm of each of these X,Y,Z vectors provides the amplitude of the FOD along the corresponding peak direction.
>>  
>> Also, I would like to know whether 100 directions are good enough to estimate the directions of three fibers.
>> 
>> 
>> Yes, that's more than enough. In my experience, 60 is already enough for lmax 8.
>>  
>> Cheers,
>> 
>> Donald.
>> 
>> 
>>  
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>> 
>> 
>> 
>> -- 
>> Jacques-Donald Tournier (PhD)
>> Brain Research Institute, Melbourne, Australia
>> Tel: +61 (0)3 9496 4078
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> 
> 
> 
> 
> -- 
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9496 4078

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