Hi Aifeng,<br><br>As I mentioned in another thread, AIR/MUT in DtiStudio is designed for intra-DTI motion correction. Suppose you have 1 b0 and 30 DWIs, all DWIs can be registered to the b0.<br><br>In your case, you want to do cross-modality (T1 vs DTI) registration. I recommend you to use DiffeoMap for that purpose. This program is designed for intra-subject cross-modality (the same person, different scans) or inter-subject image registration, which you are interested in.<br>
<br>The "adjust the gradient ..." option is for intra-DTI registration. If each DWI is not registered and motion-corrected, you need to recalculate the gradient table, strictly speaking. We usually do not use this option, but sometime reviewers ask if you recalculate the table. <br>
<br><div class="gmail_quote">On Fri, Jul 9, 2010 at 4:49 PM, Zhang, Aifeng <span dir="ltr"><<a href="mailto:azhang@psych.uic.edu">azhang@psych.uic.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Dear DTIStudio,</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Just want to double check with you about my procedure with one
DTI sequence and one MPRAGE:</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">In DTIStudio:</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">1) MRI view3D: register MPRAGE image (voxel size 0.83X0.83X1.1mm)
to b0 image (0.83X0.83X2.2mm) using affine transformation.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">2) DTI Mapping: register all DWIs to b0 using affine too. </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">3) Fiber-tracking: draw ROI on co-registered MPRAGE images for fiber
tracking.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">in step 2: do you recommend choosing the option of "Adjusting
the gradients of the DWI images if applicable"???</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">thanks for your help!</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Sincerely,</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Aifeng</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> <a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>
[mailto:<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>] <b>On Behalf Of </b>susumu mori<br>
<b>Sent:</b> Thursday, July 08, 2010 8:01 PM<br>
<b>To:</b> Zhang, Aifeng<br>
<b>Subject:</b> Re: [Mristudio-users] Eddy_current_correction</span></p>
</div>
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom: 12pt;">Yes. Usually all DWIs to b0.</p>
<div>
<p class="MsoNormal">On Thu, Jul 8, 2010 at 8:37 PM, Zhang, Aifeng <<a href="mailto:azhang@psych.uic.edu" target="_blank">azhang@psych.uic.edu</a>> wrote:</p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Dr. Mori,</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">thanks for quick response. So I
will register 32 gradients to b0 for all my data.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">I don't have error message
problem. (maybe it's someone else?)</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">thanks! </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Aifeng</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-color: -moz-use-text-color;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> <a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a> [mailto:<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>] <b>On
Behalf Of </b>susumu mori<br>
<b>Sent:</b> Thursday, July 08, 2010 7:30 PM<br>
<b>To:</b> Zhang, Aifeng</span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 10pt;"><br>
<b>Subject:</b> Re: [Mristudio-users] Eddy_current_correction</span></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom: 12pt;">Do you
still have the error message problem?<br>
Because coregistration smooths the data and SNR changes, it is a good idea to
apply it to all data.</p>
<div>
<p class="MsoNormal">On
Thu, Jul 8, 2010 at 8:08 PM, Zhang, Aifeng <<a href="mailto:azhang@psych.uic.edu" target="_blank">azhang@psych.uic.edu</a>>
wrote:</p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Dear DTIStudio,</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Is coregistration always recommended as
the first step, as I saw from articles from your lab? In our case, we only
acquired 1 DTI sequence with 32 directions (~4 mins, with SENSE 2.5).
thanks.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Sincerely,</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Aifeng</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-color: -moz-use-text-color;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> <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>On Behalf Of </b>susumu mori<br>
<b>Sent:</b> Wednesday, June 30, 2010 9:32 PM</span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 10pt;"><br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] Eddy_current_correction</span></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom: 12pt;">When
you load the REC file using "Mri3DView", make sure how many images
are in the file. For example, if you used Philips "High" table, you
have 1 b0 + 32 DWI + 1 extra image, total 34 images. The last one is an
isotropically-weighted image generated from the DWIs. Then make sure your
gradient table. Most likely, the number of images in your REC and the gradient
table are not matching.<br>
<br>
For example, you may have only 33 lines in the table. For the final image,
which you don't use, you can add an extra line with 33: 100, 100, 100. The
first "33" is the line number (34th table row), and "100, 100,
100" sends a message to DtiStudio "don't use this image".</p>
<div>
<p class="MsoNormal">On
Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades <<a href="mailto:Seyede.Ghazal.Mohades@vub.ac.be" target="_blank">Seyede.Ghazal.Mohades@vub.ac.be</a>>
wrote:</p>
<p class="MsoNormal">>Dear
all<br>
I have a completely basic question<br>
when I try to load Philips Rec images in DTI studio I can do it, however the
same set file (which is a DTI ss-EPI sequence )gives the following error
when I try to do DTI mapping :<br>
the file is Bigger (and sometimes it says smaller)than a DWI sequence!<br>
where is the problem?<br>
regards<br>
Ghazal<br>
>Thanks<br>
><br>
>-----Original Message-----<br>
>From: <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
on behalf of <a href="mailto:support@mristudio.org" target="_blank">support@mristudio.org</a><br>
>Sent: Mon 6/28/2010 12:24 PM<br>
>To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
>Subject: Re: [Mristudio-users] Eddy_current_correction<br>
><br>
>the 1st method would be fine: use the 1st B0 as a reference and register
all<br>
>others with it.<br>
><br>
>support<br>
><br>
><br>
><br>
>><br>
>> Hi All,<br>
>><br>
>> We have diffusion data set acquired with 5 trails/repetitions(in
single time<br>
>> point/cross sectional) for each and every subject. This means i have 5
b0(same<br>
>> value) and DW (12 directions) data while doing eddy current correction
can i<br>
>> choose for instance b0 from first trail and register all the DW and
other b0<br>
>> images to this or do eddy current correction separately for each and
every trail<br>
>> and finally register all of them together say for instance to the
first trail.<br>
>><br>
>> Thanks<br>
>><br>
>> venkat<br>
>><br>
>> ===================================<br>
>><br>
>> P Please consider the environment before printing this e-mail<br>
>><br>
>> Cleveland Clinic is ranked one of the top hospitals<br>
>> in America by U.S.News & World Report (2009).<br>
>> Visit us online at <a href="http://www.clevelandclinic.org" target="_blank">http://www.clevelandclinic.org</a> for<br>
>> a complete listing of our services, staff and<br>
>> locations.<br>
>><br>
>><br>
>> Confidentiality Note: This message is intended for use<br>
>> only by the individual or entity to which it is addressed<br>
>> and may contain information that is privileged,<br>
>> confidential, and exempt from disclosure under applicable<br>
>> law. If the reader of this message is not the intended<br>
>> recipient or the employee or agent responsible for<br>
>> delivering the message to the intended recipient, you are<br>
>> hereby notified that any dissemination, distribution or<br>
>> copying of this communication is strictly prohibited. If<br>
>> you have received this communication in error, please<br>
>> contact the sender immediately and destroy the material in<br>
>> its entirety, whether electronic or hard copy. Thank you.<br>
>> _______________________________________________<br>
>> Mristudio-users mailing list<br>
>> <a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
>> <a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
>> Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
>><br>
><br>
><br>
>_______________________________________________<br>
>Mristudio-users mailing list<br>
><a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
><a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
>Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
><br>
><br>
><br>
>===================================<br>
><br>
>P Please consider the environment before printing this e-mail<br>
><br>
>Cleveland Clinic is ranked one of the top hospitals<br>
>in America by U.S.News & World Report (2009).<br>
>Visit us online at <a href="http://www.clevelandclinic.org" target="_blank">http://www.clevelandclinic.org</a>
for<br>
>a complete listing of our services, staff and<br>
>locations.<br>
><br>
><br>
>Confidentiality Note: This message is intended for use<br>
>only by the individual or entity to which it is addressed<br>
>and may contain information that is privileged,<br>
>confidential, and exempt from disclosure under applicable<br>
>law. If the reader of this message is not the intended<br>
>recipient or the employee or agent responsible for<br>
>delivering the message to the intended recipient, you are<br>
>hereby notified that any dissemination, distribution or<br>
>copying of this communication is strictly prohibited. If<br>
>you have received this communication in error, please<br>
>contact the sender immediately and destroy the material in<br>
>its entirety, whether electronic or hard copy. Thank you.<br>
><br>
><br>
<br>
<br>
_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">mristudio-users-unsubscribe@mristudio.org</a></p>
</div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><br>
_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">mristudio-users-unsubscribe@mristudio.org</a></p>
</div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> </p>
</div>
</div>
<br>_______________________________________________<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/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org">mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br>