[Mristudio-users] DTIStudio isn't reading headers correctly

Tue Nov 24 17:29:35 EST 2009

obrigada

________________________________
From: susumu mori <susumu at mri.jhu.edu>
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>
Cc: wmcgarry at gmu.edu
Sent: Tue, November 24, 2009 8:26:55 PM
Subject: Re: [Mristudio-users] DTIStudio isn't reading headers correctly

Judy is right. I think you did two signal averaging.
For DTI, Siemens scanners do not actually average data and save them into separate files. So if you do 2 signal averaging of 13 DWI+b0 scans, you get 26 Mosaic files. Below, I provide some related info you may be interested in.

1) In regular MR scans, such as T1 and T2, signal averaging is done in time-domain data (called k-space) with so-called phase-cycling. For example, if you do 2 averaging, the actual data in the time domain looks inverted. If one seems to have a positive k-space peak, the other has a negative peak. These two data are acquired in a way that they are completely opposite. When the actual averaging is done, they are subtracted, not added; a - (-a) = 2a, suppose "a" is the signal. They do this to remove consistent noise. Suppose the non-random consistent noise (such as leakage of certain radio signal into the scanner), the first scan signal becomes a+b (b = noise) and the second scan is -a+b. If you subtract these two (a+b) - (-a+b) = 2a; you can see that the consistent noise is canceled out.

2) In DTI, there is a reason that you can't do this "time domain (k-space) averaging". This is because of physiological motion such as pulsation. If you do two scans and one is denoted as "a", then the second scan becomes "a*", in which "*" means some phase inconsistency among the scans due to motion. Note that this motion-caused phase inconsistency is due to very tiny tissue motion. Much smaller than the pixel size, which can not be suppressed unless the subject is dead. Because of this issue, you can not use the phase-cycling approach; a - (-a*) is not equal to 2a. As a result, DTI scans do not do k-space (time-domain) averaging. They calculate image first; the time domain signal "a" is converted to image "A". Because after magnitude image calculation, phase information is discarded, the second scan "a*" also becomes "A". So, you can do simple signal averaging A + A = 2A, in the image domain.

3) Now, once the time domain data "a" or "a*" are converted to image "A", we may ask, "what the point of creating 2A by adding two images?".  Please note that once you calculate the magnitude image "A", you can not expect to cancel out the consistent noise "b" like the time-domain averaging. Such noise just keeps adding up. Creating 2A images, on the other hand, have negative impacts. For example, if the subject moved between the two scans, you can not do image registration anymore once the two scans are added. If one of the images are corrupted and two images are added, both images get corrupted. Therefore, it is a good idea to keep the two images stored separately. 

4) Going back to your problem, you need to create a new table like;

0: 0.000, 0.000, 0.000
 1: 1.000, 0.414, -0.414
 2: 1.000, -0.414, -0.414
 3: 1.000, -0.414, 0.414
 4: 1.000, 0.414, 0.414
 5: 0.414, 0.414, 1.000
 6: 0.414, 1.000, 0.414
 7: 0.414, 1.000, -0.414
 8: 0.414, 0.414, -1.000
 9: 0.414, -0.414, -1.000
 10: 0.414, -1.000, -0.414
 11: 0.414, -1.000, 0.414
 12: 0.414, -0.414, 1.000
 13: 0.000, 0.000, 0.000
 14: 1.000, 0.414, -0.414
 15: 1.000, -0.414, -0.414
 16: 1.000, -0.414, 0.414
 17: 1.000, 0.414, 0.414
 18: 0.414, 0.414, 1.000
 19: 0.414, 1.000, 0.414
 20: 0.414, 1.000, -0.414
 21: 0.414, 0.414, -1.000
 22: 0.414, -0.414, -1.000
 23: 0.414, -1.000, -0.414
 24: 0.414, -1.000, 0.414
 25: 0.414, -0.414, 1.000

, which is a simple repeated copy of the 12-orientation table, or submit two separate scans rather than two signal averaging, from which you will get two separate directories, each contain 13 images. In this case, you can list the two directories as the sources of data and use 

0: 0, 0, 0
1:  1.000000, 0.414250, -0.414250 
2:  1.000000, -0.414250, -0.414250 
3:  1.000000, -0.414250, 0.414250 
4:  1.000000, 0.414250, 0.414250
5:  0.414250, 0.414250, 1.000000
6:  0.414250, 1.000000, 0.414250
7:  0.414250, 1.000000, -0.414250
8:  0.414250, 0.414250, -1.000000
9:  0.414250, -0.414250, -1.000000
10:  0.414250, -1.000000, -0.414250
11:  0.414250, -1.000000, 0.414250
12:  0.414250, -0.414250, 1.000000

The former dataset is considered as one set of 26 DWI+b0 data. The latter will be considered as (13 DWI+b0)x2 data. The advantage of the second approach is that DtiStudio can provide you subtracted images of the two sets, from which you can get idea about patient motion.

I hope it helps.

Susumu

On Tue, Nov 24, 2009 at 3:57 PM, Judy James <JJames2 at radiology.umsmed.edu> wrote:

How many averages have you collected your data with?
>>Some scanners if the mosaic option is turned on, will collect images twice instead of averaging it into 1 data set and this can cause 12 directions x 2 avg. + 1(b0) x 2 avg. = 26 sets of images.
>
>>Judy
>
>
>>*****************************************************
>>Dr. Judy Rose James
>>MR Physicist/Assistant Professor
>>Department of Radiology
>>University of Mississippi Medical Centre
>>Jackson, MS 39216
>>Ph: 601-984-2585
>>Pager: 601-929-2442
>>email: jjames2 at radiology.umsmed.edu
>>*****************************************************
>>>>> Ryan <wmcgarry at gmu.edu> 11/24/09 2:42 PM >>>
>
>I'm encountering some trouble where DTIStudio isn't reading my headers
>>correctly. I have MRI data collected with an Allegra scanner. It
>>contains a b0 with 12 directions, but 26 appear in the drop-down list
>>on the "Image" tab. I would greatly appreciate any ideas people may
>>have. Thanks.
>>   -Ryan
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