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:<br>
<br>fslroi my_peaks.nii first_peak 0 3<br><br>and to get the second largest peak:<br>fslroi my_peaks.nii second_peak 2 3<br><br>and finally the third:<br>fslroi my_peaks.nii third_peak 6 3<br>
<br>(I am sure you can substitute fslroi for mrcat for similar operations)<br><br>You can visualize them as lines in fslview.<br><br>Luis<br><br><br><br><div class="gmail_quote">On Thu, Oct 18, 2012 at 3:11 PM, David Raffelt <span dir="ltr"><<a href="mailto:d.raffelt@brain.org.au" target="_blank">d.raffelt@brain.org.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Peter, <div>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.</div>
<div>Cheers,</div><div>Dave<div><div class="h5"><br><br><div class="gmail_quote">On 19 October 2012 00:43, Peter Neher <span dir="ltr"><<a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Dave,<br>
<br>
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?<br>
<br>
Best,<br>
Peter<div><div><br>
<br>
<br>
<div>On 10/18/2012 11:37 AM, David Raffelt
wrote:<br>
</div>
<blockquote type="cite">Hi Peter,
<div>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.</div>
<div>
<br>
</div>
<div>Note that dir2amp can be used to convert these directions to
peak amplitudes.</div>
<div>Cheers,</div>
<div>Dave</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<br>
<div class="gmail_quote">On 18 October 2012 19:06, Peter Neher <span dir="ltr"><<a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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?<br>
<br>
Best<br>
Peter<br>
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<div><font color="#ff6600">Post Doctoral Fellow</font></div>
<div><br>
</div>
<div>The Florey Institute of Neuroscience and Mental Health</div>
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<br>
</div></div><span><font color="#888888"><pre cols="72">--
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
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</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><b><font color="#ff6600">Dr David Raffelt</font></b></div><div><font color="#ff6600">Post Doctoral Fellow</font></div><div><br></div><div>The Florey Institute of Neuroscience and Mental Health</div>
<div>Melbourne Brain Centre - Austin Campus</div><div>245 Burgundy Street</div><div>Heidelberg Vic 3084<div>Ph: <a value="+61390357024">+61 3 9035 7024</a></div></div><div><a value="+61390357024">www.florey.edu.au</a></div>
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