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<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>Dear Susumu,</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>I would like to thank you
and all other, for the detailed answers. </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>The interpretation of the
data is indeed problematic, since in some patients we get the CC in the u shape
and in other we don't. It seems that the comparison of the mean values of FA,
MD and eigen values of the CC, is wrong. In addition, the parameter of the size
of the CC obtained from the number of fibers in the reconstructed fiber is also
unreliable. We found it to be highly dependent on the one who make the
tractography, while the mean of the other parameters are much more repeatable. </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks again</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>Dafna</span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><br>
</span></font><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Thank you very much for the detailed explanation</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'> </span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
lang=SV style='font-size:10.0pt;font-family:"Courier New";color:navy'>Dafna Ben
Bashat Ph.D. </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
lang=SV style='font-size:10.0pt;font-family:"Courier New";color:navy'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>Senior
Physicist, In charge of MR systems</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>The Wohl
institute for Advanced Imaging</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>Brain Imaging
Center</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>Tel Aviv Sourasky
Medical Center</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>Phone:
972-3-6973953 (o) Fax:
972-3-6973080</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>
972-52-4262515 (m) Mail:
dafnab@tasmc.health.gov.il</span></font></p>
</div>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'> </span></font></p>
<div>
<div class=MsoNormal align=center dir=LTR style='text-align:center'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>susumu mori<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, March 11, 2010
11:49 PM<br>
<b><span style='font-weight:bold'>To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users] CC
in elderly patients</span></font></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal dir=LTR style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>No I don't. My research
is application-driven and I haven't requested by any application to resolve
fibers within a pixel to answer an important clinical question.<br>
<br>
Most of application research is talking about inter-pixel or pixel-cluster
anatomical information (e.g. what is the size of a structure) but not intra-pixel
information (e.g. how much water population is going up-down and how much in
right-left).</span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On Thu, Mar 11, 2010 at 3:45 PM, Jun Yi Wang <<a
href="mailto:junyiwang2002@yahoo.com">junyiwang2002@yahoo.com</a>> wrote:</span></font></p>
<div>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi Susumu,<br>
<br>
Just realized that I have a question to ask: are you working on a way to handle
the crossing fiber issue such as the two-tensor streamline tractography
proposed by Qazi et al. (2009), NeuroImage 47:T98-106?<br>
<br>
Jun Yi</span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<div>
<div class=MsoNormal align=center dir=LTR style='text-align:center'><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
<hr size=1 width="100%" align=center>
</span></font></div>
<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Jun Yi
Wang <<a href="mailto:junyiwang2002@yahoo.com" target="_blank">junyiwang2002@yahoo.com</a>></span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'><br>
<b><span style='font-weight:bold'>To:</span></b> "DTI Studio, ROI Editor,
Landmarker Questions/Support" <<a
href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a>></span></font></p>
</div>
<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>Sent:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Thu,
March 11, 2010 12:34:50 PM</span></font></p>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users] CC
in elderly patients</span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi Susumu,<br>
<br>
Thank you very much for the detailed explanation! It is very
useful. I have the same impression of the difficulty of defining a gold
standard for tractography after I read the paper by Dauguet et al. (2007):
Comparison of fiber tracts derived from in-vivo DTI tractography with 3D
histological neural tract tracer reconstruction in a macaque brain.<br>
<br>
Jun Yi</span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<div>
<div class=MsoNormal align=center dir=LTR style='text-align:center'><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
<hr size=1 width="100%" align=center>
</span></font></div>
<p class=MsoNormal dir=LTR style='margin-bottom:12.0pt'><b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> susumu
mori <<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>><br>
<b><span style='font-weight:bold'>To:</span></b> "DTI Studio, ROI Editor,
Landmarker Questions/Support" <<a
href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a>>;
Xin Li <<a href="mailto:xli16@jhmi.edu" target="_blank">xli16@jhmi.edu</a>><br>
<b><span style='font-weight:bold'>Sent:</span></b> Thu, March 11, 2010 12:01:50
PM<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users] CC
in elderly patients<br>
</span></font><br>
Hi all,<br>
<br>
We have noticed the same phenomena and also got several inquiries from outside.
Here is my understanding;<br>
<br>
1) For young subjects, the shape of the CC has a clean U shape in coronal
sections. If you do fiber tracking, you usually can reconstruct the U-shape
trajectory, which makes some anatomical sense.<br>
2) For the population with enlarged ventricles, such as elderly, AD, and stroke
patients, the trajectory of the CC becomes more like a "W" shape with
a sharp turn where the CC merges to the corona radiata. I believe that this is
the primary reason that most streamlines end up in going downward toward the
internal capsule, which doesn't make much anatomical sense. <br>
3) Think about the 90 degree rotated "T" shape and the vertical line
is the corona radiata and the horizontal line is the CC. If the horizontal line
merges at the right angle, the probability of the tracking to go upward and
downward is 50/50. If the horizontal line is slightly tiled upward, the CC
tracking merges to the vertical line (corona radiata) and continues to travel
upward. It's as simple as this. Once we get a vector (or tensor) field and ask
a computer to reconstruct a path, the computer doesn't know the anatomy. All it
knows is just a bunch of vectors. One may think that probabilistic tracking can
deal with it but the connectivity strength could be influenced by the merging
angle too.<br>
4) This exemplifies what tractography is. It is just a region growing (or
pixel-connection) tool based on pixel-by-pixel information, no matter which
algorithm we use. It is just a feature extraction tool from MRI that
observes water molecules. Some results look right and some results do not.<br>
5) Then many people ask, "how do we know the validity". Here we (both
who ask the question and who is asked the question) have to think very hard. To
show the validity, we need to compare our observation (in this case
tractography result) and gold standard (real anatomy). Then what do we really mean
by "real anatomy" or "real connectivity"? What is
connectivity anyway? First of all many of the macroscopic anatomical definition
such as "superior longitudinal fasciculs" and "corona
radiata" are defined by human eyes based on anatomical features, which
doesn't have a clear definition and boundary. It's like a cloud. Everybody can
see it at the core but at the boundary, we don't know how to define. Then how
about the microscopic anatomical definition? Yes, we have a very clear
definition, which is axonal connection. However, we know that one neuron
communicate with multiple neurons through a <b><span style='font-weight:bold'>branching</span></b>
axon. We have 100 billion neurons. Even if one neuron communicate with one
neuron, this is a 100 billion x 100 billion question. For MRI, even if you do 1,000-orientation
Q-ball imaging, we are talking about merely few GB of data. With a tensor
fitting, what we have is 20 MB. On top of it, we are measuring water
properties. So, we can understand that we are on a very shaky ground when we
talk about "validation" because we can't even define what is the gold
standard we are shooting for and our data is so small compared to what we are
interested in.<br>
6) Then next question is, "why do we do tractography". Here, we
should go back and think why we do MRI first of all and what is the real power
of it. The real power is that we can examine the entire brain within 30 min
non-invasively and quantitatively. This is something no other modality,
certainly histology, can't do. By performing a feature extraction such as tractography,
we can quickly and quantitatively assess the anatomical status.<br>
7) As long as we apply the same data acquisition method and the same analysis
method, the results itself is always correct. There is nothing wrong with the
results whatever they are. In this example, in some population, the CC goes
downward while it goes upward in the normal subjects. The tractography
sensitively detected some differences between the two population.<br>
8) If we make mistake in this situation, that is when we interpret the data.
For example, if we interpret the data like, "in young brains, the CC goes
up and in aged brain the CC goes down because the connectivity changed",
now such a statement becomes the subject of "right or wrong".<br>
9) So, it is very important to evaluate why you got different results between
two groups. The real reason could be something not the measurement was
intended. For the case of the CC trajectory, the real reason could be
"enlarged ventricles" and the DTI + tractography could be just an
expensive and indirect way to show it.<br>
10) This is a very typical issue in MRI, not just DTI. When we observe cortical
thinning in T1, it may be just a change in contrast due to myelination status
or other things. What we really observe is the thinning of T1-indicated-cortical-compartment
and the direct translation into the real cortical thickness is sometimes
dangerous or even erroneous. As long as we are dealing with 10 MB of water
information, biological or cellular interpretation always requires caution.<br>
11) Fiber reconstruction is a high-level image analysis tool, which is
sensitive to so many anatomical factors including both micro and macroscopic
factors. The microscopic factors are myelination, axonal loss, cellular loss,
edema, etc that would affect the FA and anatomy. The microscopic factors are
multiple compartments (e.g. crossing fibers) within the 2 mm pixel. So, in
general, the interpretation would be difficult. It is a good tool to survey the
overall white matter anatomy but you need to exercise the caution when you
interpret it.<br>
<br>
<br>
I guess what I mentioned above contains a lot of my personal opinions and
please take it as just one of the opinions, but hope it helps to understand the
issue of the downard CC projection.<br>
<br>
Susumu<br>
<br>
</p>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On Thu, Mar 11, 2010 at 11:52 AM, Jun Yi Wang <<a
href="mailto:junyiwang2002@yahoo.com" target="_blank">junyiwang2002@yahoo.com</a>>
wrote:</span></font></p>
<div>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi Dafna,<br>
<br>
I only have a few subjects in 80s, but I have subjects from 16-65 years
old. I do see a substantial decrease of the amount of corpus callosum
fibers projecting towards the cortex as we age. Some fibers still project
to the cortex although a lot of them project downwards instead. I don't
know whether this is caused by aging or DTI artifacts such as the termination
of line propagation because of the lower FA or the crossing fiber issue.<br>
<br>
Jun Yi Wang</span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><span style='-moz-background-clip: border;
-moz-background-origin: padding;-moz-background-inline-policy: continuous;
background-attachment:scroll;background-position-x:0%;background-position-y:
0%'>Postdoctoral Research Scholar</span></span></font><font size=2
face=sans-serif><span style='font-size:10.0pt;font-family:sans-serif'><br>
Fragile X Research and Treatment Center<br>
</span></font>UC Davis M.I.N.D. Institute<br>
530.747.3808 (Lab)</p>
<div>
<div class=MsoNormal align=center dir=LTR style='text-align:center'><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
<hr size=1 width="100%" align=center>
</span></font></div>
<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Dafna Ben
Bashat <<a href="mailto:dafnab@tasmc.health.gov.il" target="_blank">dafnab@tasmc.health.gov.il</a>><br>
<b><span style='font-weight:bold'>To:</span></b> <a
href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<b><span style='font-weight:bold'>Sent:</span></b> Thu, March 11, 2010 3:19:20
AM<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] CC in
elderly patients</span></font></p>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi all,</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>We are currently working on data from elderly stroke/TIA
patients. </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>In many of the TIA patients, who have good DTI data, for
some reason the CC does not built well, we can't see the fan. </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>This is not due to incorrect directions (the CST is built
OK).</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>ROI measurements give reasonable values. We even changed the
flip-angel for the FACT, and got the same results.</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Any suggestions? Is it a known phenomenon in elderly /
stroke / TIA patients? </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thank you in advance.</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dafna </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
embed'><font size=2 face=Arial><span dir=LTR style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Dafna Ben Bashat Ph.D. </span></font></p>
<p class=MsoNormal dir=LTR><span dir=LTR></span><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><span dir=LTR></span> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Senior Physicist, In
charge of MR systems</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>The Wohl institute for
Advanced Imaging</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Brain Imaging Center</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Tel Aviv Sourasky Medical
Center</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Phone: 972-3-6973953
(o) Fax: 972-3-6973080</span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> </span></font></p>
<p class=MsoNormal dir=LTR><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
972-52-4262515 (m) Mail: <a
href="mailto:dafnab@tasmc.health.gov.il" target="_blank">dafnab@tasmc.health.gov.il</a></span></font></p>
<p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span dir=LTR style='font-size:12.0pt'> </span></font></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span lang=HE
dir=RTL style='font-size:12.0pt'> </span></font></p>
</div>
<p class=MsoNormal dir=LTR style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
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