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Tanks for your help! Looks good.<br>
<br>
<div class="moz-cite-prefix">On 10/18/2012 10:22 PM, Luis Concha
wrote:<br>
</div>
<blockquote
cite="mid:CAOq9ZoFdW0iDARpKPe3Cyw_n04ox7BDDPamSZ5GPzVwtVmoxJg@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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>
<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 moz-do-not-send="true"
value="+61390357024">+61 3 9035 7024</a></div>
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value="+61390357024">www.florey.edu.au</a></div>
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</blockquote>
<br>
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<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
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a moz-do-not-send="true" href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a moz-do-not-send="true" href="http://www.dkfz.de" target="_blank">www.dkfz.de</a>
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.</pre>
</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 moz-do-not-send="true"
value="+61390357024">+61 3 9035 7024</a></div>
</div>
<div><a moz-do-not-send="true" value="+61390357024">www.florey.edu.au</a></div>
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</div>
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</blockquote>
</div>
<br>
</blockquote>
<br>
<pre class="moz-signature" 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
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:p.neher@dkfz-heidelberg.de">p.neher@dkfz-heidelberg.de</a>, Web: <a class="moz-txt-link-abbreviated" href="http://www.dkfz.de">www.dkfz.de</a>
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.</pre>
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