Hi Susumu and Xin, many thanks. It works great.<div><br></div><div>Siewmin<br><br><div class="gmail_quote">On Sat, May 2, 2009 at 1:10 AM, susumu <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" 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 Siewmin,</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">I hope Xin is working on the error message
you got. </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">I just want to comment on your
"Screenshot1". In this window, the template is T1 and your data to be
normalized is FA. </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">I recommend to use the same contrast. For
example, you can use b0 (T2) or DWI for both template and your data. </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">There are two ways to normalize FA;</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">1) you can load both DWI (or b0) and FA. Choose
DWI in active window before you start AIR. After AIR all leaded images (in this
case FA) will also be normalized based on the DWI-DWI (or b0-b0) intra-contrast
AIR result. Avoid cross-contrast AIR as much as possible.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">2) you can do DWI-DWI (or b0-b0) AIR and
save the AIR output file (transformation matrix). Later, you can load FA, ADC,
or whatever images you want to normalize. Then apply the AIR transformation
matrix using the button with "M coming out of a folder" button in the
"Volume LDDMM" section.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<div>
<div 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>Siewmin Gan<br>
<b><span style="font-weight:bold">Sent:</span></b> Friday, May 01, 2009 1:35 AM<div><div></div><div class="h5"><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]
question using AIR in Landmarker</div></div></span></font></p>
</div><div><div></div><div class="h5">
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Xin thanks. I have attached a few shots here with a brief
description.</span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">1. the landmarker window where I clicked on the "align
button" at the bottom left corner</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">2. The folder where I would save the output file (filename:
AlignWarpOutput and filetype:(*.warp)). This folder is in my Computer/Local
Disk/Landmarker (i.e C:/Landmarker) where I have placed the Landmarker software
and the .exe files.</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">3. In snapshot 3, i change the save as type file to all files, so you
can see that the align_warp.exe and other .exe files are also in this folder.</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">4. The snapshot of the 1st error msg. When I clicked "OK",
the second error message occur as shown in shot 5. </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Initially, I did get a warning message that there should be no spaces
in the whole path of the warp file etc, and have resolved that error
message. </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Many Thanks</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Siewmin </span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On Fri, May 1, 2009 at 12:02 AM, Xin Li <<a href="mailto:xli16@jhmi.edu" target="_blank">xli16@jhmi.edu</a>> wrote:</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Siewmin,<br>
<br>
Could you take snapshots of these two error messages? And please tell me the
whole path of the warp file that you were going to save on your machine. The
whole path of the warp file should not have any spaces. I am not sure if this
is the reason.</span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
<br>
Xin<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: Siewmin Gan <<a href="mailto:siewmin.gan@gmail.com" target="_blank">siewmin.gan@gmail.com</a>></span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Date: Thursday, April 30, 2009 11:31 am<br>
Subject: Re: [Mristudio-users] question using AIR in Landmarker<br>
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a>><br>
<br>
<br>
> Hi Xin, the error message occurs in a pop up warning window on the
DTIstudio<br>
> GUI.<br>
> thanks<br>
><br>
> Siewmin<br>
><br>
> On Wed, Apr 29, 2009 at 11:30 PM, Xin Li <<a href="mailto:xli16@jhmi.edu" target="_blank">xli16@jhmi.edu</a>> wrote:<br>
><br>
> > Siewmin,<br>
> ><br>
> > Where did you see this error message
"C:/Landmarker/align_warp.exe.<br>
> The<br>
> > parameter is incorrect" ? Did you see it in the C command
window or<br>
> in a pop<br>
> > up warning window?<br>
> ><br>
> ><br>
> > Xin<br>
> ><br>
> ><br>
> ><br>
> > ----- Original Message -----<br>
> > From: Siewmin Gan <<a href="mailto:siewmin.gan@gmail.com" target="_blank">siewmin.gan@gmail.com</a>><br>
> > Date: Thursday, April 23, 2009 5:08 am<br>
> > Subject: [Mristudio-users] question using AIR in Landmarker<br>
> > To: <a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
> ><br>
> ><br>
> > > Hi, I'm trying to do non-linear registration
to normalise my resampled<br>
> > > aDWI images to the ICBM_DTI_81 DWI template. When I
clicked on the<br>
> > "align<br>
> > > button", I recieved two error messages (below),
and could not perform<br>
> > > the<br>
> > > registration step:<br>
> > ><br>
> > > "C:/Landmarker/align_warp.exe. The parameter is
incorrect"<br>
> followed by<br>
> > > "cannot find warp file".<br>
> > ><br>
> > > I have placed the aligned_warp.exe file in the
folder landmarker<br>
> where<br>
> > > software is located, and am not sure where the
problem may be.<br>
> > ><br>
> > > Many Thanks<br>
> > ><br>
> > > Siewmin<br>
> > > _______________________________________________<br>
> > > Mristudio-users mailing list<br>
> > > <a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
> > ><br>
> > _______________________________________________<br>
> > Mristudio-users mailing list<br>
> > <a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
> ><br>
> ><br>
> _______________________________________________<br>
> Mristudio-users mailing list<br>
> <a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
><br>
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