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<div class="moz-cite-prefix">Dear all<br>
<br>
Just a short comment about the first point : Using nifti file for
DWI data is very convenient especially when one use other software
to do the dti preprocessing (eddy current correction and epi
unwarping). Waiting for the next mrtrix version (where it may be
available ?) I use fsl to do the dti preprocessing and I wrote a
small matlab code that take the 4D nifti DTI volume with bval and
bvecs and on the gradient table in mrtrix format (and I apply the
rotation of the nifti file to the bvec)<br>
<br>
cheers<br>
<br>
Romain<br>
<br>
Le 28/08/2012 04:25, Donald Tournier a écrit :<br>
</div>
<blockquote
cite="mid:CAPP9hqQ8XyCbT2kfUimUSu6wFjffdVoJ--WTDJeKLptEvAcjnw@mail.gmail.com"
type="cite">Hi Chris,
<div><br>
</div>
<br>
<div>On a different note: in the process of looking at the data
you sent over, I had a quick look through your script. There's a
few things I'd like to mention, which I think others might also
want/need to hear. Here goes:</div>
<div><br>
</div>
<div><b>Using NIfTI to store the DWI data:</b></div>
<div><b><br>
</b></div>
I notice you're supplying a NIfTI image for the DWI, and a
separate gradient encoding file. While there's nothing wrong with
that per se, you need to make double-sure that your encoding file
is correct <i>for each scan</i>. MRtrix assumes gradients are in
the scanner coordinate system (also typically assumed in DICOM
data - exception being GE), whereas FSL expects assumes they are
in the image axes coordinate system. These two won't match if the
images are acquired in a non-axial or oblique plane, and in
general won't match between scans even if acquired using the same
protocol. This rotation needs to be accounted for when converting
between bvecs/bvals and the MRtrix encoding file. I assume you've
probably already sorted that out, but thought I'd flag this issue
again just in case.
<div>
<br>
</div>
<div>I would strongly recommend that everyone convert their data
directly from the raw DICOM images to .mif (or .mih) format,
since the gradient information will then be read directly by
MRtrix and stored in the appropriate format within the image
header - no need to supply the encoding file separately, which
gets rid of a potential source of user error. </div>
<div><br>
</div>
<div><b>Use of -normalise option in csdeconv:</b></div>
<div><br>
</div>
<div>I strongly advise <i>against</i> the use of the -normalise
option of estimate_response. Although the response function
might be normalised, the FODs derived using csdeconv will not be
(unless also processed using -normalised, but that introduces
other issues with CSF contamination, <a moz-do-not-send="true"
href="http://www.nitrc.org/pipermail/mrtrix-discussion/2012-July/000472.html">as
discussed previously in this thread</a>). Using a
non-normalised response function and non-normalised csdeconv
actually produces relatively well normalised FODs, since the
response is then scaled appropriately for the DW signal.</div>
<div><br>
</div>
<div><b>Use of gen_WM_mask:</b></div>
<div><br>
</div>
<div>I also strongly advise against the use of gen_WM_mask. It's a
bit of a Heath Robinson hack job, using fairly arbitrary
heuristics to kinda identify voxels that ought to correspond to
white matter - not really based on sound principles. I included
it in the original release as I thought it would provide a good
rough mask of WM to seed from, but it's since become clear that
it doesn't work all that well, and produces variable results
depending on the SNR, b-value, and number of directions. In
hindsight, I shouldn't have included in the release, and it
won't be available in future major releases.</div>
<div><br>
</div>
<div><br>
</div>
<div><b>Creating the mask:</b></div>
<div><br>
<div>The command you use creates a mask from a single b=0 image.
A more robust approach, now recommended in the documentation,
is to use the average of all volumes in the DWI run -
basically improves the SNR:</div>
<div><br>
</div>
<div>
<div>$ average dwi.mif -axis 3 - | threshold - - | median3D -
- | median3D - mask.mif</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><b>Getting the single-fibre mask:</b></div>
<div><br>
</div>
<div>This is another command that has changed in recent
versions. No big deal, but the current recommended command is:</div>
<div><br>
</div>
<div> $ erode mask.mif -npass 3 - | mrmult fa.mif - - |
threshold - -abs 0.7 sf.mif</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>That's all I had to say. Just thought I'd take the
opportunity to clarify a few things...</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald</div>
<div><br>
</div>
<div><br>
<div><br>
<div class="gmail_quote">On 27 August 2012 12:18, Donald
Tournier <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@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
Chris,
<div><br>
</div>
<div>I can't think of much that could cause this
problem, but the most obvious one is supplying an
empty single-fibre mask at the estimate_response step.
Another reason might have been if any of the
single-fibre voxels has one or more zero DW
intensities - but I've just looked at the code, and
there are safeguards in place to handle negative or
zero DW intensities, so I can't see that it could be
that either. If none of this helps, maybe you can send
me one of the offending data sets so I can have look?</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
Donald.</div>
<div>
<div>
<div class="h5"><br>
<br>
<div class="gmail_quote">On 27 August 2012 11:57,
Chris Adamson <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:chris.adamson@mcri.edu.au"
target="_blank">chris.adamson@mcri.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">Donald,<br>
<br>
I am getting NaN values in the response.txt
file in rare cases. How can<br>
I diagnose the problem/fix it? What should I
look for in the data that<br>
would cause a failure of the ellipse fitting?<br>
<br>
Chris.<br>
--<br>
Dr Christopher Adamson, PhD (Melb.), B
Software Engineering (Hons.,<br>
Monash)<br>
Research Officer<br>
Developmental Imaging, Critical Care and
Neurosciences<br>
<br>
Murdoch Childrens Research Institute<br>
The Royal Children’s Hospital<br>
Flemington Road Parkville Victoria 3052
Australia<br>
T 9906 6780<br>
M XXXX XXX XXX<br>
E <a moz-do-not-send="true"
href="mailto:chris.adamson@mcri.edu.au"
target="_blank">chris.adamson@mcri.edu.au</a><br>
<a moz-do-not-send="true"
href="http://www.mcri.edu.au"
target="_blank">www.mcri.edu.au</a><br>
<br>
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<br>
<br clear="all">
<div><br>
</div>
</div>
</div>
<span class="HOEnZb"><font color="#888888">-- <br>
<font color="#ff6600" size="1"><b>Dr
Jacques-Donald Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">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>
<div><font size="1">Heidelberg Vic 3084</font></div>
<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>
<br>
<br>
</font></span></div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">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>
<div><font size="1">Heidelberg Vic 3084</font></div>
<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">www.florey.edu.au</a></font></div>
<br>
<br>
</div>
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