[Mristudio-users] Coregistration using AIR

[Jun Yi Wang]

Hi All,
 
I have followup questions regarding the AIR program in DTI Studio.
 
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?
 
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?
 
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?
 
Thank you for your wonderful tools and timely support!
Jun Yi Wang



----- Original Message ----
From: susumu <susumu at mri.jhu.edu>
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>
Sent: Friday, July 25, 2008 11:09:48 AM
Subject: Re: [Mristudio-users] Coregistration using AIR


Dear Dr. Takaya,
 
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.
 
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).
 
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).
 
Susumu
 

________________________________

From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shigetoshi TAKAYA
Sent: Monday, July 14, 2008 1:48 AM
To: Mristudio-users at mristudio.org
Subject: [Mristudio-users] Coregistration using AIR
 
Hello
 
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.
 
First, I did eddy current correction and motion correction using affine transformation in each scan (1st scan and 2nd scan).
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.
 
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?
 
Many thanks,
 
Shigetoshi Takaya


      
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