Dear Susumu<font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">,<br><br>I also have a similar question about </span></font><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">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<br>
<br><div class="gmail_quote">2009/4/16 susumu <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="blue" lang="EN-US">
<div>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Hi Eric,</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; 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></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p style="margin-left: 0.5in; text-indent: -0.25in;"><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"><span>1)<font size="1" face="Times New Roman"><span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></font></span></span></font><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Gradient table: High (32-orientation)/ Medium (15-orientation) /
Low (6-orientation)</span></font></p>
<p style="margin-left: 0.5in; text-indent: -0.25in;"><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"><span>2)<font size="1" face="Times New Roman"><span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></font></span></span></font><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Overplus (ON / OFF)</span></font></p>
<p style="margin-left: 0.5in; text-indent: -0.25in;"><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"><span>3)<font size="1" face="Times New Roman"><span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></font></span></span></font><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Oblique plane (X/Y/Z angles)</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; 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></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; 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></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">To simplify the DTI processing, we recommend
Overplus = NO.</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; 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></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Please let us know which options you are
using.</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Susumu</span></font></p>
<p><font color="navy" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<div>
<div style="text-align: center;" align="center"><font size="3" face="Times New Roman"><span style="font-size: 12pt;">
<hr align="center" size="2" width="100%">
</span></font></div>
<p><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; 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<div class="im"><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>
</div><b><span style="font-weight: bold;">Subject:</span></b> Re: [Mristudio-users]
Gradient table</span></font></p>
</div><div><div></div><div class="h5">
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;"> </span></font></p>
<p style="margin-bottom: 12pt;"><font size="2" face="Verdana"><span style="font-size: 10pt; 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>
<br>
</span></font></p>
<div style="text-align: center;" align="center"><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;">
<hr align="center" size="2" width="100%">
</span></font></div>
<p style="margin-bottom: 12pt;"><font size="2" face="Verdana"><span style="font-size: 10pt; 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></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: blue;">Hi Hugh,</span></font></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: blue;">When you
got this error, please suspect one of the following two reasons;</span></font></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: blue;">1)
Memory shortage:</span></font></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; 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></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: blue;">2)
Mismatch between the gradient table and the number of images:</span></font></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; 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></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: blue;">If any
of these do not solve the issue, please let us know.</span></font></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<p><span><font color="blue" size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: blue;">Susumu</span></font></span><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"> </span></font></p>
<div style="text-align: center;" align="center"><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;">
<hr align="center" size="2" width="100%">
</span></font></div>
<p style="margin-bottom: 12pt;"><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; 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><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p style="margin-bottom: 12pt;"><font size="2" face="Verdana"><span style="font-size: 10pt; 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></p>
<div style="text-align: center;" align="center"><font size="2" face="Verdana"><span style="font-size: 10pt; font-family: Verdana;">
<hr align="center" size="2" width="100%">
</span></font></div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Liang Wang, PhD<br>Postdoctoral Fellow<br>Woodward Lab<br>Department of Psychiatry<br>University of British Columbia<br>BC Mental Health & Addiction Services<br>938 West 28th Avenue<br>
Vancouver BC V5Z 4H4<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><br>