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<DIV dir=ltr align=left><SPAN class=794555907-25102010><FONT face=Arial
color=#0000ff size=2>There in the header, i think</FONT></SPAN></DIV><BR>
<DIV class=OutlookMessageHeader lang=de dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>Von:</B> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <B>Im Auftrag von </B>Wu,
Joseph<BR><B>Gesendet:</B> Freitag, 22. Oktober 2010 19:15<BR><B>An:</B> DTI
Studio, ROI Editor, DiffeoMap Questions/Support<BR><B>Betreff:</B>
[Mristudio-users] Need GE 3 tesla 25 direction DTI gradient tableplease,
thanks<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV class=WordSection1>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 11pt; COLOR: #1f497d; FONT-FAMILY: 'Calibri','sans-serif'">Hi
<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 11pt; COLOR: #1f497d; FONT-FAMILY: 'Calibri','sans-serif'">Does
somebody have GE 3 tesla 25 direction DTI gradient table that they can
forward to : <A href="mailto:jcwu@uci.edu">jcwu@uci.edu</A>? That would be
greatly appreciated. <o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 11pt; COLOR: #1f497d; FONT-FAMILY: 'Calibri','sans-serif'">Thanks,<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 11pt; COLOR: #1f497d; FONT-FAMILY: 'Calibri','sans-serif'">Joe<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 11pt; COLOR: #1f497d; FONT-FAMILY: 'Calibri','sans-serif'"><o:p> </o:p></SPAN></P>
<DIV>
<DIV
style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; PADDING-LEFT: 0in; PADDING-BOTTOM: 0in; BORDER-LEFT: medium none; PADDING-TOP: 3pt; BORDER-BOTTOM: medium none">
<P class=MsoNormal><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">From:</SPAN></B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <B>On Behalf Of </B>Xu
Li<BR><B>Sent:</B> Thursday, October 21, 2010 8:18 AM<BR><B>To:</B> DTI Studio,
ROI Editor, DiffeoMap Questions/Support<BR><B>Subject:</B> Re: [Mristudio-users]
problems with gradients<o:p></o:p></SPAN></P></DIV></DIV>
<P class=MsoNormal><o:p> </o:p></P>
<P class=MsoNormal>Dear Susumu,<o:p></o:p></P>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>I have a quick question about the gradient table I got from
the gradient_table_creator<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>It gives me a table with the [0 0 0] and [100 100 100] at the
bottom which seems to be different than those sample gradient table I have from
DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips systems
do the b0 scan at the end instead of at the beginning now?<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>Thanks!<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>Xu<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P>
<DIV>
<DIV>
<P class=MsoNormal>On Oct 20, 2010, at 10:19 PM, susumu mori
wrote:<o:p></o:p></P></DIV>
<P class=MsoNormal><BR><BR><o:p></o:p></P>
<P class=MsoNormal>Hi Jill,<o:p></o:p></P>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>I'm second to SC. When you are using Philips, even if you
thought that you are using exactly the same parameters, you could end up in two
different types of the gradient tables; overplus on and off. This is not
recorded in the beginning of PAR file.<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>So my suggestion is, try the "overplus on" option of the
table calculator.<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal>Also, if you find that you used "overplus on", you have to
type in the oblique angle information in the calculator. The angle information
is in the PAR file.<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>The reason you didn't get the tractography right is most
likely due to "+/-" signs of the gradient table you used. You can test "x/y/z
flip" function of the tractography to test it. The best way is to use the
gradient calculator, which should be able to sort out all the
issues.<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>Susumu<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P>
<DIV>
<P class=MsoNormal>On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill <<A
href="mailto:JZwicker@cw.bc.ca">JZwicker@cw.bc.ca</A>> wrote:<o:p></o:p></P>
<DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: 'Tahoma','sans-serif'">Further
to this message, the ROI values I get are consistent with the previous scans, so
it is just the fiber tracking that I am suspicious
of...</SPAN><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">Thanks!</SPAN><o:p></o:p></P></DIV>
<DIV>
<DIV class=MsoNormal style="TEXT-ALIGN: center" align=center>
<HR align=center width="100%" SIZE=2>
</DIV>
<P class=MsoNormal><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">From:</SPAN></B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'"> <A
href="mailto:mristudio-users-bounces@mristudio.org"
target=_blank>mristudio-users-bounces@mristudio.org</A> [<A
href="mailto:mristudio-users-bounces@mristudio.org"
target=_blank>mristudio-users-bounces@mristudio.org</A>] On Behalf Of Zwicker,
Jill [<A href="mailto:JZwicker@cw.bc.ca"
target=_blank>JZwicker@cw.bc.ca</A>]<BR><B>Sent:</B> October 19, 2010 1:26
PM<o:p></o:p></SPAN></P>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'"><BR><B>To:</B> DTI
Studio, ROI Editor, DiffeoMap Questions/Support<o:p></o:p></SPAN></P></DIV>
<P class=MsoNormal style="MARGIN-BOTTOM: 12pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">Subject:</SPAN></B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'"> Re:
[Mristudio-users] problems with gradients</SPAN><o:p></o:p></P></DIV>
<DIV>
<DIV>
<DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: 'Tahoma','sans-serif'">Hi
Susumu and SC,</SPAN><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">You previously
helped me with a tensor calc issue (see below). I have since used the gradient
calculator and obtained more RAM, and have successfully analyzed two scans.
However, the remaining scans are not processing properly (i.e., I do not get a
proper colour map). In looking at the PAR files, the parameters are the same as
the first two scans, with the exception of the rescale and scale slopes, window
center and widths, and diffision parameters (nothing that changes what I enter
to the online gradient table calculator). Since the gradient table I was using
didn't work for successive scans, I took the gradients from the PAR file. This
seemed to work, but the colours were reversed, so I switched coloumns around and
got a seemingly accurate colour map. However, when I tried to fiber track, the
CST seems too short and the values are not consistent with what I obtained in
the previous 2 scans.</SPAN><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">So...I am unsure why
the previous gradient table didn't work and I don't think my trial and error
method of getting a colour map is accurate. I would be happy to send you the PAR
files (off the listserv) if that would help.</SPAN><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">Thank you in advance
for your guidance.</SPAN><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">Jill</SPAN><o:p></o:p></P></DIV>
<DIV>
<DIV class=MsoNormal style="TEXT-ALIGN: center" align=center><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">
<HR align=center width="100%" SIZE=2>
</SPAN></DIV>
<P class=MsoNormal style="MARGIN-BOTTOM: 12pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'">From:</SPAN></B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Tahoma','sans-serif'"> <A
href="mailto:mristudio-users-bounces@mristudio.org"
target=_blank>mristudio-users-bounces@mristudio.org</A> [<A
href="mailto:mristudio-users-bounces@mristudio.org"
target=_blank>mristudio-users-bounces@mristudio.org</A>] On Behalf Of susumu
mori [<A href="mailto:susumu@mri.jhu.edu"
target=_blank>susumu@mri.jhu.edu</A>]<BR><B>Sent:</B> September 1, 2010 6:25
PM<BR><B>To:</B> DTI Studio, ROI Editor, DiffeoMap
Questions/Support<BR><B>Subject:</B> Re: [Mristudio-users] problems with tensor
calc</SPAN><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal>I suspect memory problem. <o:p></o:p></P>
<DIV>
<P class=MsoNormal>Please use stricter threshold (like FA>0.3 and angle
<30, for example) to see if it works. If it works, then it's memory problem
(I mean, you need more memory).<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>You can also save eigenvector0 and FA, close DtiStudio, and
redo fiber tracking using the saved file. If you start from tensor calculation,
you have all the raw data in your memory.<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal>32-bit operating system can allocate only 1-1.5GB memory.
64bit is much better.<o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><o:p> </o:p></P></DIV>
<DIV>
<P class=MsoNormal style="MARGIN-BOTTOM: 12pt">susumu<o:p></o:p></P>
<DIV>
<P class=MsoNormal>On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill <<A
href="mailto:JZwicker@cw.bc.ca" target=_blank>JZwicker@cw.bc.ca</A>>
wrote:<o:p></o:p></P>
<P class=MsoNormal>Thank you so much! After some trial and error, I figured out
the correct gradient table. I can now get a beautiful colour map, but I have a
new problem. The program crashes everytime I try to do fibre tracking. Any
suggestions?<o:p></o:p></P>
<DIV>
<DIV>
<P class=MsoNormal style="MARGIN-BOTTOM: 12pt"><BR>-----Original
Message-----<BR>From: <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>] On Behalf Of
[Seongjin]<BR>Sent: Wednesday, September 01, 2010 10:56 AM<BR>To: DTI Studio,
ROI Editor, DiffeoMap Questions/Support<BR>Subject: Re: [Mristudio-users]
problems with tensor calc<BR><BR>Use the following link for the gradient table
calculation.<BR>You need to get some information required to fill in from Par
file of your data.<BR>If your data is not in ParRec format, get it
first.<BR><BR><A
href="http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html"
target=_blank>http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html</A><BR><BR>-SC.<BR><BR>On
Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill <<A
href="mailto:JZwicker@cw.bc.ca" target=_blank>JZwicker@cw.bc.ca</A>>
wrote:<BR>> Hi DTI Studio users,<BR>><BR>> I am relatively new to DTI
studio and have been using successfully to do<BR>> tractography on infant
brain data collected on a Seimens. I am now trying to<BR>> analyze child
brain data collected on a Philips. I can get a clear image,<BR>> but as soon
as I try a tensor calculation, the image quality degrades<BR>> significantly
(no matter what the background noise level I set it to). I<BR>> made gradient
tables from the PAR file (forwards and backwards) and also<BR>> flipped the z
as the tutorial suggests. Any suggestions on how I can solve<BR>> this
problem?<BR>><BR>> Thanks for your help.<BR>><BR>><BR>><BR>>
Jill Zwicker, PhD, OT(C)<BR>><BR>> Postdoctoral Fellow<BR>><BR>>
Child & Family Research Institute<BR>><BR>> Developmental
Neurosciences & Child Health<BR>><BR>> L408 - 4480 Oak
Street<BR>><BR>> Vancouver, BC V6H 3V4<BR>><BR>> Phone:
604-875-2000 ext 6805<BR>><BR>> Fax: 604-875-3569<BR>><BR>> <A
href="mailto:jzwicker@cw.bc.ca"
target=_blank>jzwicker@cw.bc.ca</A><BR>><BR>><BR>><BR>>
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<P class=MsoNormal><o:p> </o:p></P></DIV></DIV></DIV></DIV></DIV></DIV>
<P class=MsoNormal
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class=MsoNormal>_______________________________________________<BR>mristudio-users
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