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<div class="moz-cite-prefix">Hello<br>
<br>
If it can be useful ...<br>
<br>
attached is the code (to be place in your matlab path)<br>
the main fonction to be called within matlab is
transform_bvec_to_mrtrix<br>
<br>
It uses spm function to select files and to read the nifti header.
I added all spm function needed <br>
but if you already have spm8 installed in your matlab file you
just need to keep transform_bvec_to_mrtrix.m<br>
tel me if something goes wrong<br>
<br>
<br>
Romain<br>
<br>
Le 04/09/2012 12:32, Donald Tournier a écrit :<br>
</div>
<blockquote
cite="mid:CAPP9hqShEVS59w0rcmHrCmaS5j2sutgJnkhRjwGVPL7PpYXsjw@mail.gmail.com"
type="cite">Hi Romain,
<div><br>
</div>
<div>This script sounds like it might be useful for other too. Any
chance you could share it...? </div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On 4 September 2012 18:44, romain
valabregue <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:romain.valabregue@upmc.fr" target="_blank">romain.valabregue@upmc.fr</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">
<div>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 type="cite">Hi Chris,
<div>
<div class="h5">
<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.Â
<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"
target="_blank">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>Â $ 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><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>
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<span><font color="#888888">-- <br>
<font color="#ff6600" size="1"><b>Dr
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</b></font>
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<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: Â +61 3 9035Â 7033</font></div>
<div><font size="1">Fax: Â +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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-- <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: Â +61 3 9035Â 7033</font></div>
<div><font size="1">Fax: Â +61 3 9035 7307</font></div>
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