[Mrtrix-discussion] csdeconv peaks

[David Raffelt]

Hi Peter,
I would suggest using more directions than SH coefficients in your FOD
image. Check out the find_SH_peaks help for more information on how the
peaks are saved. What it does not mention though is that the output peaks
are ordered by size (largest first). Sorry I'm not familiar with the FSL
peak file format, however I'm sure it would be fairly trial to code
a conversion tool up. A good place to start would be dir2amp, since this
code reads in the directions file and loops over each peak.
Cheers,
Dave

On 19 October 2012 00:43, Peter Neher <p.neher at dkfz-heidelberg.de> wrote:

>  Hi Dave,
>
> seems to work fine. Do you have any recommendation how many directions to
> generate using gendir? And can you give me the exact specification of the
> find_SH_peaks output image so that I can read it somehow using my own code?
> Or is there a conversion to the FSL peak file format?
>
> Best,
> Peter
>
>
>
> On 10/18/2012 11:37 AM, David Raffelt wrote:
>
> Hi Peter,
> You can use the find_SH_peaks command. Note that you also have to supply a
> set of directions as input, which are used as seeds for the peak finding.
> You can generate these using the gendir command.
>
>  Note that dir2amp can be used to convert these directions to peak
> amplitudes.
> Cheers,
> Dave
>
>
>
>
> On 18 October 2012 19:06, Peter Neher <p.neher at dkfz-heidelberg.de> wrote:
>
>> Hi all, I wondered if it is possible to directly output the fiber
>> directions and not only the SH representation of the ODFs. If this is not
>> possible, can anyone tell me how the SH file looks like so that I can read
>> it and extract the peaks myself?
>>
>> Best
>> Peter
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>
>
>
>  --
> *Dr David Raffelt*
> Post Doctoral Fellow
>
>  The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7024
>  www.florey.edu.au
>
>
> --
> Dipl.-Inform. Peter Neher
> German Cancer Research Center
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-- 
*Dr David Raffelt*
Post Doctoral Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7024
www.florey.edu.au
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