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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Liang,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><span
style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>I
am not sure which coordinates (space) the ultimate gradient table was relative
to, such as frequency- and phase-encoding of image, horizontal and vertical
direction of image, or magnets' x/y/z coordinates. Based on your reply, I think
that it might be the last one.<font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>When you present vectors, color maps, or performing
fiber tracking, X, Y, and Z need to be defined by the image matrix. This is the
most natural way. The frequency/phase/slice and image x/y/z have permutation
relationship, like frequency – image x / phase – image y / slice –
image z or frequency – image y / phase – image x / slice – image
z.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>The relationship between magnet x / y / z and image x
/ y / z could have oblique relationship if oblique scan is used, and therefore
could be very complicated.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>The gradient table, ultimately, needs to adopt the
image x / y / z system. Now most vendor system is adopting a way to deliver
gradient application in the frequency/phase/slice system, moving away from
gradient x/y/z. This means, when oblique scan is employed, the scanner
dynamically recalculates the gradient table in the f/p/s coordinates. If the
scanner doesn’t do this (like old Siemens system), we have to recalculate
the table based on the oblique angles by ourselves. The former is more fool-proof.<br>
<br>
2) In my *.PAR file, there was last 3 columns representing diffusion directions
but obviously different between subjects. I don't know what diffusion were
recorded in this header file.<font color=navy><span style='color:navy'><o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>I don’t have much experience with the new PAR
file, but if you are using oblique scans, it is not surprising the each patient
have different gradient table in the “magnet” coordinate. Suppose
we want to apply [1, 0, 0] in the first line of the gradient table, which is the
“X” orientation. If we use an oblique scan, magnet X and image X
are no longer the same. As I mentioned above, in the end, what we want to know
is gradient orientation in the image coordinate. So we have two choices. <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Choice 1: deliver magnet [1, 0, 0], meaning pure X
gradient application. This X gradient could be something like [0.9, 0.15, 0] in
the image coordinate. We need to do [1, 0, 0] x ImageRotation to get new
gradient table to do tensor calculation.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Choice 2: deliver magnet [0.9, -0.15, 0] (I just made
up these numbers) so that the applied gradient aligns the image X axis. In this
case, we can use gradient table [1, 0, 0] for tensor calculation.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.25in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>I hope this makes your questions answered.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>Susumu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
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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><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>liang wang<br>
<b><span style='font-weight:bold'>Sent:</span></b> Saturday, April 18, 2009
2:42 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]
Gradient table</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Dear Susumu</span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>,<br>
<br>
I also have a similar question about gradient tables in Philips scanner</span></font>.
<br>
<br>
My data were collected using following protocols:<br>
1) Gradient table: Medium<br>
2) Gradient overplus: no<br>
3) Oblique plane: yes, and different angles between subjects.<br>
<br>
Looking through your answer, I know that this set can result in the same
gradient table input into DTIstudio for all subject. However, 1) I am not sure
which coordinates (space) the ultimate gradient table was relative to, such as
frequency- and phase-encoding of image, horizontal and vertical direction of
image, or magnets' x/y/z coordinates. Based on your reply, I think that it
might be the last one.<br>
<br>
2) In my *.PAR file, there was last 3 columns representing diffusion directions
but obviously different between subjects. I don't know what diffusion were
recorded in this header file.<br>
<br>
Many thanks<br>
<br>
Liang<o:p></o:p></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>2009/4/16 susumu <<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>><o:p></o:p></span></font></p>
<div link=blue vlink=blue>
<div>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>Hi Eric,</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>For Philips scanner there are several types of gradient
tables you can specify in the scanner. Please check your protocol for the
following points;</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p style='margin-left:.5in;text-indent:-.25in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>1)</span></font><font
size=1 color=navy><span style='font-size-adjust: none;font-stretch: normal'><span
style='font-size:7.0pt;color:navy'> </span></span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Gradient table: High (32-orientation)/ Medium (15-orientation) /
Low (6-orientation)</span></font><o:p></o:p></p>
<p style='margin-left:.5in;text-indent:-.25in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>2)</span></font><font
size=1 color=navy><span style='font-size-adjust: none;font-stretch: normal'><span
style='font-size:7.0pt;color:navy'> </span></span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Overplus (ON / OFF)</span></font><o:p></o:p></p>
<p style='margin-left:.5in;text-indent:-.25in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>3)</span></font><font
size=1 color=navy><span style='font-size-adjust: none;font-stretch: normal'><span
style='font-size:7.0pt;color:navy'> </span></span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Oblique plane (X/Y/Z angles)</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>The first option has 3 choices and the second option has 2
choices. Therefore, there are 3 x 2 = 6 gradient tables.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>If the second option (Overplus) is NO, the third option has
no effect. If the second option is YES, the gradient table has to be rotated
based on the oblique angles.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>To simplify the DTI processing, we recommend Overplus = NO.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>We have the basic 6 tables, which can be used as is if you
use Overplus = OFF or Oblique angles = 0/0/0 degree.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>Please let us know which options you are using.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>Susumu</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p><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'> <a
href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
<b><span style='font-weight:bold'>On Behalf Of </span></b>eric Q<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, April 16, 2009
9:44 PM<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma'><br>
<b><span style='font-weight:bold'>To:</span></b> <a
href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>Subject:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Re:
[Mristudio-users] Gradient table</span></font><o:p></o:p></p>
</div>
<div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p style='margin-bottom:12.0pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Hello Dear DTIstudio users:<br>
<br>
I am new to DTIstudio, I was hoping someone could give me some much needed
advises for beginners.<br>
<br>
<br>
I was trying to obtain the FA values for my brain phantom (PHILIP 3T scanner).
When I clicked on "DTI mapping", it prompted me to enter the
"gradient table", how do I calculate the "gradient table"?<br>
<br>
Thanks in advanced<br>
<br>
Best regards<br>
<br>
Eric<br>
<br>
</span></font><o:p></o:p></p>
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face=Verdana><span style='font-size:10.0pt;font-family:Verdana'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p style='margin-bottom:12.0pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Date: Thu, 9 Apr 2009 11:04:09
-0400<br>
From: <a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a><br>
To: <a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
Subject: Re: [Mristudio-users] MriView3D application close</span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>Hi Hugh,</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>When you got this error, please suspect one of the following
two reasons;</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>1) Memory shortage:</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>Even if you have many GB of memories, 32-bit Windows system
can allocate only 1 - 1.5 GB to each program. To check if you have the memory
problem, please restrict the slices to be calculated. In the
initial data parameter window, there is a section called "Slices to
be processed". Here you can specify only a portion of slices to be
processed. Please limit the slices to, for example, 0-9 and see how it goes. If
you can calculate tensors without errors, then you have the memory problem. The
solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2
batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch),
calculate all maps (e.g. FA), and later combine them.</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>2) Mismatch between the gradient table and the number of
images:</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>For example, if you specify 12-orientation table and 30
volume images, then you get the error. After loading the data and before you go
to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down
menu in the right column of the Image tab. If you have the correct number of
the images, then you might have an error in your gradient table. Small mistakes
such as missing "," are often difficult to detect. The best way is;
a) load the data using DtiMapping under the "File" button on the top
left, b) close the window, c) open the image paremater window again by clicking
"DtiMapping" in the "File" button again, d) the window still
remembers the gradient table you entered last time. This remembered window
tells how DtiStudio interpreted your gradient table. If there is any syntax
errors, you may find them much easier. For example, if you enter, "4: 1
0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4:
1, 0, 0".</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>If any of these do not solve the issue, please let us know.</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
<p><font size=2 color=blue face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:blue'>Susumu</span></font><o:p></o:p></p>
<p><font size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> </span></font><o:p></o:p></p>
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face=Verdana><span style='font-size:10.0pt;font-family:Verdana'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p 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'> <a
href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
<b><span style='font-weight:bold'>On Behalf Of </span></b>Hugh Wang<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, April 08, 2009
6:30 PM<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'>Subject:</span></b> [Mristudio-users]
MriView3D application close</span></font><o:p></o:p></p>
<p style='margin-bottom:12.0pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Hi, <br>
<br>
I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM
diffusion images (1baseline,64 gradients). After successfully loading the
images, I click the "dti map" option at lower right corner. Whatever
calculation I choose, it always gives me an error: <br>
<br>
"MriView3D MFC Application has encountered a problem and needs to
close. We are sorry for the inconvenience."<br>
<br>
I tried several PCs, and the problem keeped the same. I would appreciate that
if there's anyone having any idea on how to solve it. Thanks.<br>
<br clear=all>
Best,<br>
Hugh</span></font><o:p></o:p></p>
<div class=MsoNormal align=center style='text-align:center'><font size=2
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</span></font></div>
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_______________________________________________<br>
Mristudio-users mailing list<br>
<a href="mailto:Mristudio-users@mristudio.org">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br clear=all>
<br>
-- <br>
Liang Wang, PhD<br>
Postdoctoral Fellow<br>
Woodward Lab<br>
Department of Psychiatry<br>
<st1:place w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:PlaceName
w:st="on">British Columbia</st1:PlaceName></st1:place><br>
BC Mental Health & Addiction Services<br>
<st1:Street w:st="on"><st1:address w:st="on">938 West 28th Avenue</st1:address></st1:Street><br>
<st1:place w:st="on"><st1:City w:st="on">Vancouver</st1:City> <st1:State w:st="on">BC</st1:State>
<st1:PostalCode w:st="on">V5Z 4H4</st1:PostalCode></st1:place><br>
Telephone: 1-604-875-2000 (ext. 4735)<br>
Fax: 1-604-875-3871<br>
Email: <a href="mailto:wanglbit@gmail.com">wanglbit@gmail.com</a><o:p></o:p></span></font></p>
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