[Mrtrix-discussion] csdeconv peaks

[Peter Neher]

Tanks for your help! Looks good.

On 10/18/2012 10:22 PM, Luis Concha wrote:
> Once you get your peaks image, you can use fslroi to extract each set 
> of peaks. For example, if you found tree peaks per voxel, the 4th 
> dimension of your file should have 9 elements (3 peaks, each with xyz 
> components). So, to get the first peak, you would invoke:
>
> fslroi my_peaks.nii first_peak 0 3
>
> and to get the second largest peak:
> fslroi my_peaks.nii second_peak 2 3
>
> and finally the third:
> fslroi my_peaks.nii third_peak 6 3
>
> (I am sure you can substitute fslroi for mrcat for similar operations)
>
> You can visualize them as lines in fslview.
>
> Luis
>
>
>
> On Thu, Oct 18, 2012 at 3:11 PM, David Raffelt <d.raffelt at brain.org.au 
> <mailto:d.raffelt at brain.org.au>> wrote:
>
>     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
>     <mailto: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
>>         <mailto: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
>         (DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
>         Division of Medical and Biological Informatics
>         Im Neuenheimer Feld 280, D-69120 Heidelberg
>
>         Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
>         E-Mail:p.neher at dkfz-heidelberg.de  <mailto:p.neher at dkfz-heidelberg.de>, Web:www.dkfz.de  <http://www.dkfz.de>
>
>         The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
>
>
>
>
>     -- 
>     *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
>
>
>     _______________________________________________
>     Mrtrix-discussion mailing list
>     Mrtrix-discussion at www.nitrc.org
>     <mailto:Mrtrix-discussion at www.nitrc.org>
>     http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>

-- 
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: p.neher at dkfz-heidelberg.de, Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

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