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<div class="moz-cite-prefix">Hello Donald,<br>
<br>
Thank you for your reply. Regarding your first question, I was
feeding all 3 shells, I was not aware this was not supported in
MRtrix. Is there no way of utilising all the information from the
3 shells at present?<br>
<br>
As for the second part, you are entirely correct, it seems to be
an incorrect FOD causing the program to keep looking for a start
point. I re-computed with FOD with a single shell (b=3000), and
streamtrack is back to working fine. <br>
<pre class="moz-signature" cols="72">Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH</pre>
On 13/01/13 22:57, Donald Tournier wrote:<br>
</div>
<blockquote
cite="mid:CAPP9hqQOd7rku2w2RP3Gv+zhi=gKd2NcfDf-pV=G201PoscfFA@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Chris & Ivan,
<div><br>
</div>
<div>OK, I think there are a few issues to consider here. The
first thing is to figure out why the response function estimated
for these data is not right. Are you using just a single shell
of the HARDI data, or are you simply feeding all 3 shells to
MRtrix? MRtrix is only designed to handle single shell data, so
if you're doing the latter, it's no surprise that it will have
issues. It may be possible to analyse these kinds of data in a
future version, but for now you should stick to single-shell
HARDI, unfortunately.</div>
<div><br>
</div>
<div>As to why the tracking hangs: the most likely reason is that
the program is failing to find a suitable seed point. The
procedure in MRtrix is to select a random point and a random
orientation, compute the FOD amplitude, and start tracking if
that amplitude is greater than the -init_cutoff threshold (by
default, 0.2). If your response function is incorrect, there is
a good chance that the scaling of the resulting FODs will also
be off, giving you smaller FODs than expected - in which case
streamtrack will try in vain to find a single suitable seed
point/orientation, and appear to hang. To verify this, you could
try using a -cutoff value of zero to see if that at least
produces tracks. You could also use the find_SH_peaks command on
the CSD output file, and check the FOD peak amplitudes (although
it's a little more work to figure out how to extract the
amplitude from that).</div>
<div><br>
</div>
<div>If none of this helps, I'm happy to have a look at the data -
usually quicker to troubleshoot that way...</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald.</div>
<div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On 12 January 2013 02:49, Parker,
Christopher <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:christopher.parker.10@ucl.ac.uk"
target="_blank">christopher.parker.10@ucl.ac.uk</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">
<div
style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi
Ivan and Mrtrix users,
<div><br>
</div>
<div>I have just experienced the same problem with
streamtrack SD_PROB. It does not produce any
streamlines and hangs although still uses a lot of
CPU. I think it might have something to do with the
SH harmonic coefficient file (source argument in
streamtrack), since when I use a harmonic
coefficient file from a different scan it works fine
(all other arguments were the same files). I need to
find a solution to this also.</div>
<div><br>
</div>
<div>Best,</div>
<div>Chris<br>
<div style="font-size:16px;font-family:Times New
Roman">
<hr>
<div style="direction:ltr"><font color="#000000"
face="Tahoma"><b>From:</b> <a
moz-do-not-send="true"
href="mailto:mrtrix-discussion-bounces@www.nitrc.org"
target="_blank">mrtrix-discussion-bounces@www.nitrc.org</a>
[<a moz-do-not-send="true"
href="mailto:mrtrix-discussion-bounces@www.nitrc.org"
target="_blank">mrtrix-discussion-bounces@www.nitrc.org</a>]
on behalf of Ivan Alvarez [<a
moz-do-not-send="true"
href="mailto:ivan.alvarez.11@ucl.ac.uk"
target="_blank">ivan.alvarez.11@ucl.ac.uk</a>]<br>
<b>Sent:</b> 09 January 2013 15:03<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:mrtrix-discussion@www.nitrc.org"
target="_blank">mrtrix-discussion@www.nitrc.org</a><br>
<b>Subject:</b> [Mrtrix-discussion] Human
Connectome Project dataset issue<br>
</font><br>
</div>
<div>Hello Mrtrix users,<br>
<br>
I tried analysing a sample subject from the
recently available Human Connectome Project
dataset (<a moz-do-not-send="true"
href="https://db.humanconnectome.org"
target="_blank">https://db.humanconnectome.org</a>),
and encountered an issue with CSD tractography
in Mrtrix. In brief, the dataset has 1.25 mm
isotropic voxels, 270 directions, 3 b-shells
(1000,2000,300) and 2 repeats.<br>
<br>
The tensor estimation worked fine, and am able
to compute sensible-looking FA maps. The mask
erosion is also fine, but when I view the
response function coefficient, it displays an
unusual shape (<a moz-do-not-send="true"
href="http://postimage.org/image/cl7tpwc3p/"
target="_blank">RCF</a>). The csdeconv command
returns no errors and the orientation plot looks
reasonable. My problem is, when I attempt to
perform tractography with the streamtrack
command, the program hangs.<br>
<br>
Any idea as to why this might be?<span
class="HOEnZb"><font color="#888888"><br>
<pre cols="72">--
Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH</pre>
</font></span></div>
</div>
</div>
</div>
</div>
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<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<font size="1" color="#ff6600"><b>Dr Jacques-Donald Tournier<br>
</b></font>
<div><font size="1" color="#ff6600">Research Fellow</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">The Florey Institute of Neuroscience and
Mental Health</font></div>
<div><font size="1">Melbourne Brain Centre - Austin Campus</font></div>
<div><font size="1">245 Burgundy Street</font></div>
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<div><font size="1">Ph: +61 3 9035 7033</font></div>
<div><font size="1">Fax: +61 3 9035 7307</font></div>
<div><font size="1"><a moz-do-not-send="true"
href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
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