[Mristudio-users] using T1 image for ROI drawing

Zhang, Aifeng azhang at psych.uic.edu
Tue Jul 13 12:20:50 EDT 2010 

Hi Hangyi

So I tried with Mutual-info registration and it works just fine on MPRAGE and aligned well with b0 images. and I also found that the fibers come out better using mutual-info registration on DWIs.  So is mutual-info reg a better choice?

thanks,
Aifeng

-----Original Message-----
From: Hangyi Jiang [mailto:hjiang at jhmi.edu] 
Sent: Tuesday, July 13, 2010 9:49 AM
To: Zhang, Aifeng
Subject: RE: using T1 image for ROI drawing

hi, Aifeng,

AIRed images will have same FOV and dimensions with that of the reference image. the slices-shifting is the result of the image registration, so the program try to align two images together.  it is not the problem, it is the job that AIR supposed to do.

however,  AIR may not do the job well (that is why image registration is a very active research field).  basically, if AIR can correct motion artifacts between the images of same modality very well.  since MPRAGE and B0 (and DWIs) are acquired in different ways,  the image intensities (or contract) might be different for same anatomical regions, AIR may not work well.   that is why we recommend using B0 (not MPRAGE) as a reference to register DWIs.  


best,

hangyi


________________________________________
From: Zhang, Aifeng [azhang at psych.uic.edu]
Sent: Monday, July 12, 2010 6:39 PM
To: Hangyi Jiang
Subject: RE: using T1 image for ROI drawing

hi Hangyi,

my AIR co-registered MPRAGE(axial) to b0(axial) have couple slices shifted in head-to-toe direction.  It seems like  the original MPRAGE doesn't have the same FOV and image center.  Could you please tell me what procedure can solve this problem when those two sequences have different FOV and image center?  Thanks a lot!

Sincerely,
Aifeng

-----Original Message-----
From: Hangyi Jiang [mailto:hjiang at jhmi.edu]
Sent: Monday, July 12, 2010 8:48 AM
To: Zhang, Aifeng
Subject: RE: using T1 image for ROI drawing

basically, the procedures are right.

in step 3,  ROIs are mostly defined on color map or FA map, besides on MPRAGE

hangyi


________________________________________
From: Zhang, Aifeng [azhang at psych.uic.edu]
Sent: Saturday, July 10, 2010 11:39 PM
To: Hangyi Jiang
Subject: RE: using T1 image for ROI drawing

Thanks, so the rest of my procedure is correct?

Sincerely,
Aifeng

Sent from my Windows Mobile(r) phone.

-----Original Message-----
From: Hangyi Jiang <hjiang at jhmi.edu>
Sent: Saturday, July 10, 2010 8:34 PM
To: Zhang, Aifeng <azhang at psych.uic.edu>
Subject: RE: using T1 image for ROI drawing


yes, "Adjusting the gradients" is needed.

hangyi



________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zhang, Aifeng [azhang at psych.uic.edu]
Sent: Friday, July 09, 2010 4:49 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] using T1 image for ROI drawing

Dear DTIStudio,

Just want to double check with you about my procedure with one DTI sequence and one MPRAGE:

In DTIStudio:
1) MRI view3D: register MPRAGE image (voxel size 0.83X0.83X1.1mm) to b0 image (0.83X0.83X2.2mm) using affine transformation.
2) DTI Mapping: register all DWIs to b0 using affine too.
3) Fiber-tracking: draw ROI on co-registered MPRAGE images for fiber tracking.

in step 2:  do you recommend choosing the option of "Adjusting the gradients of the DWI images if applicable"???

thanks for your help!

Sincerely,
Aifeng

From: smoriw at gmail.com [mailto:smoriw at gmail.com] On Behalf Of susumu mori
Sent: Thursday, July 08, 2010 8:01 PM
To: Zhang, Aifeng
Subject: Re: [Mristudio-users] Eddy_current_correction

Yes. Usually all DWIs to b0.
On Thu, Jul 8, 2010 at 8:37 PM, Zhang, Aifeng <azhang at psych.uic.edu<mailto:azhang at psych.uic.edu>> wrote:
Dr. Mori,

thanks for quick response.  So I will register 32 gradients to b0 for all my data.

I don't have error message problem.  (maybe it's someone else?)

thanks!
Aifeng

From: smoriw at gmail.com<mailto:smoriw at gmail.com> [mailto:smoriw at gmail.com<mailto:smoriw at gmail.com>] On Behalf Of susumu mori
Sent: Thursday, July 08, 2010 7:30 PM
To: Zhang, Aifeng

Subject: Re: [Mristudio-users] Eddy_current_correction

Do you still have the error message problem?
Because coregistration smooths the data and SNR changes, it is a good idea to apply it to all data.
On Thu, Jul 8, 2010 at 8:08 PM, Zhang, Aifeng <azhang at psych.uic.edu<mailto:azhang at psych.uic.edu>> wrote:
Dear DTIStudio,

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.

Sincerely,
Aifeng

From: mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org> [mailto:mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org>] On Behalf Of susumu mori
Sent: Wednesday, June 30, 2010 9:32 PM

To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Eddy_current_correction

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.

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".
On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades <Seyede.Ghazal.Mohades at vub.ac.be<mailto:Seyede.Ghazal.Mohades at vub.ac.be>> wrote:
>Dear all
I have a completely basic question
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 :
the file is Bigger (and sometimes it says smaller)than a DWI sequence!
where is the problem?
regards
Ghazal
>Thanks
>
>-----Original Message-----
>From: mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org> on behalf of support at mristudio.org<mailto:support at mristudio.org>
>Sent: Mon 6/28/2010 12:24 PM
>To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>Subject: Re: [Mristudio-users] Eddy_current_correction
>
>the 1st method would be fine: use the 1st B0 as a reference and register all
>others with it.
>
>support
>
>
>
>>
>> Hi All,
>>
>> We have diffusion data set acquired with 5 trails/repetitions(in single time
>> point/cross sectional) for each and every subject. This means i have 5 b0(same
>> value) and DW (12 directions) data while doing eddy current correction can i
>> choose for instance b0 from first trail and register all the DW and other b0
>> images to this or do eddy current correction separately for each and every trail
>> and finally register all of them together say for instance to the first trail.
>>
>> Thanks
>>
>> venkat
>>
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>P Please consider the environment before printing this e-mail
>
>Cleveland Clinic is ranked one of the top hospitals
>in America by U.S.News & World Report (2009).
>Visit us online at http://www.clevelandclinic.org for
>a complete listing of our services, staff and
>locations.
>
>
>Confidentiality Note:  This message is intended for use
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>and may contain information that is privileged,
>confidential, and exempt from disclosure under applicable
>law.  If the reader of this message is not the intended
>recipient or the employee or agent responsible for
>delivering the message to the intended recipient, you are
>hereby notified that any dissemination, distribution or
>copying of this communication is strictly prohibited.  If
>you have received this communication in error,  please
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