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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 Jun,<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'>Please see my response below.<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>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>1). The
instruction stated that AIR in DTI Studio is for motion correction and eddy
current correction for multiple DTI aquisitions. So if I have DTI sequences
already averaged by the scanner, can I use the AIR to correct for motion and
eddy current?<o:p></o:p></span></font></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>>I recommend not to average scans inside the scanner. Eddy
current should be correctable even if the images are already averaged. Motion
correction is a tricky question. It depends on when the second set is acquired
and when the motion happens. In the worst case, second scan take place after
the first complete DTI is finished so that there is ½ of scanning time lapsed
between the averaging (typically several minutes). If the motion happens
between the first and second scans, then motion correction may not work well.</span></font> <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><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>2). After
the AIR process in DTI Studio, the saved matrix has corrected gradient
table. If I proceed to calculate tensor, etc., is the modified gradient
table or the original one used in the calculation? If the corrected table
is not used, should I calculate tensor by closing the DTI Studio, loading all
images, and use the modified gradient table for tensor calculation?<o:p></o:p></span></font></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>>Good question. I need Hangyi to answer this. My guess is
the corrected table is applied by default if you choose this option. Please
remember, unless you uncheck the “create new image after registration”,
AIR simply creates corrected images. The subsequent calculation still uses the
uncorrected original data. In this case, you do have to save the corrected
images & table and reload them to use them. If you unckeck this button,
then the original images are overwritten by the AIRed images. In this case, the
subsequent tensor calculation will be based on the AIRed images. Then the
gradient table should be automatically corrected (although I have to confirm
this point with Hangyi).<o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>3). I
have been using FSL's eddy_correct program, and I can hardly find any
discription for the program. Has anyone compared it with the AIR?<o:p></o:p></span></font></p>
<p><font size=3 color=navy face="Times New Roman"><span style='font-size:12.0pt;
color:navy'>> I heard FLIRT in FSL works better than AIR. One of the
AIR’s weak points is its sensitivity to the threshold setting. The
“create image …” functions in the “outlier
rejection” and calculation of subtracted images when there are more than
two repeated measurements provide very good interface to visually inspect the
existence of the mis-registration. At this point, I recommend you to confirm
the results of AIR using these functions and the the inspection window (“Original-ADC-Mean-STD”
button).</span></font><o:p></o:p></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Thank you
for your wonderful tools and timely support!<o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Jun Yi
Wang<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3 face="MS PGothic"><span
style='font-size:12.0pt'>----- Original Message ----<br>
From: susumu <susumu@mri.jhu.edu><br>
To: "DTI Studio, ROI Editor, Landmarker Questions/Support"
<mristudio-users@mristudio.org><br>
Sent: Friday, July 25, 2008 11:09:48 AM<br>
Subject: Re: [Mristudio-users] Coregistration using AIR</span></font><font
face="Times New Roman"><span style='font-family:"Times New Roman"'><o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Dr. Takaya,</span></font><o:p></o:p></p>
<p class=MsoNormal><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 class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Do you want to coregister, combine two DTI
scans and calculated a tensor? If that's the case, you can treat the two scans
as two signal averaging. Load both of them, coregister the first scan to the
second scan using the AIR in DtiStudio, and do tensor calculation.</span></font><o:p></o:p></p>
<p class=MsoNormal><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 class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>If you want to get separate tensor fields
from the two datasets and then coregister for ROI drawing, I recommend you to
use Landmarker. You first have to calculate all DTI-based images you need
(tensor, FA, ADC, b0, etc). You can then bring b0 images from the two datasets
into Landmarker and perform AIR. You can save the transformation matrix and
apply it to other images. Alternatively, if you load all data at once, AIR is
automatically applied to all loaded data (of course you have to specify which
image you want to use to drive AIR).</span></font><o:p></o:p></p>
<p class=MsoNormal><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 class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>One important function of Landmarker is
that it can apply the transformation matrix to tensor files too (it does tensor
reorientations if rotation components are involved).</span></font><o:p></o:p></p>
<p class=MsoNormal><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 class=MsoNormal><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 class=MsoNormal><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="MS PGothic"><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>Shigetoshi TAKAYA<br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, July 14, 2008 1:48
AM<br>
<b><span style='font-weight:bold'>To:</span></b> Mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users]
Coregistration using AIR</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>Hello</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>I have two scans of DWI with time interval
for each patient (1st scan and 2nd scan). I would like to coregister
the images in the 2nd scan onto those in the 1st scan
in each subject using Automatic Image Registration (AIR) algorithm implemented
in DTIStudio, for the purpose of drawing ROIs in the same brain regions in both
scans.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>First, I did eddy current correction
and motion correction using affine transformation in each scan (1st scan and
2nd scan).</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>Then, I coregistered the B0
image in the 2nd scan onto that in the 1st scan. And I
would like to adjust the same transformation matrix to the rest of
the images in the 2nd scan.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>I know that the transformation matrix can be
saved when conducting AIR. Can we use this file to transform the rest of the
images in the 2nd scan?</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>Many thanks,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="MS PGothic"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="MS UI Gothic"><span style='font-size:
12.0pt;font-family:"MS UI Gothic"'>Shigetoshi Takaya</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;font-family:"Times New Roman"'><o:p> </o:p></span></font></p>
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