[Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS

[susumu mori]

Well, I didn't mean TBSS was better than the other. Different granularity
means different sensitivity/specificity to different types of diseases.

For example, when we are studying brain growth and tissue atrophy in certain
neurodegenerative disease, it happens in a global manner. There is an
overall tendency like frontal lobe develop earlier than the occipital lobe.
When you are going after this type of changes, it doesn't make sense to use
the smallest granularity (pixel). If the change is only 5%, you can't find
it by pixel-based methods because each pixel is too noisy. TBSS may also
have too much granularity because each skeleton point may average only few
adjacent pixels. In this case, an ROI drawn in the frontal lobe and occiptal
lobe averaging thousands of pixels may be a better method.

On the other hand if a lesion is sharply localized, then you want higher
granularity.  Pixels averaging always have a danger that abnormal pixels are
averaged with normal pixels and thus dilute the effect.

Raw pixel-based data is therefore always nice to have. It has low
sensitivity and you can hardly get any statistical level once you do
multiple-pixel comparison. But if you lower the statistical thresholding,
you start to see some tendency. The filtering (pixel averaging) by TBSS may
help to bring up such information above the surface of statistical power.
However, you can also argue that if the abnormality is localized to one side
of the tract, the projection to the center of the white matter core would
decrease the sensitivity.

Also, you can also argue that the skeletanization is somewhat a blackbox
operation. When you are looking at the white matter away from the core where
there are cross-subject variability, I'm not sure how the white matter is
skeletanized and how they are aligned among subjects.

Again, VBA data is one step closer to raw data before the high order image
analysis such as TBSS do something on the pixel-by-pixel data. So you can
argue that VBA and TBSS is not A or B, it is more like A or AxB

Hope it helps.

On Fri, May 14, 2010 at 1:41 PM, lion gao <gaolion at gmail.com> wrote:

> Dear Susumu Mori,
>
> Thanks very much for your answer, it's very informative!
> One question is that when you mention granularity and anatomy, it finally
> all leads to the advantages of TBSS, the skeleton. so my answer looks a bit
> repeated for a same point. Another one is I do need to find some flaw in
> TBSS for defence use :P, so I find some limitation from the original paper.
> BTW, I am NOT familiar with TBSS.
> http://sirl.stanford.edu/~bob/pdf/DTI/Methods/Smith_TBSS_NeuroImage06.pdf<http://sirl.stanford.edu/%7Ebob/pdf/DTI/Methods/Smith_TBSS_NeuroImage06.pdf>
>
> Finally, I arranged some defences based on your comments below. Have a look
> if interested , or simply skip it :)
>
> Thanks again & Best Wishes,
> Gao
>
>
> It has been quite a time since VBA was popularly used in DTI data, while
> track-based spatial statistical gains popularity rapid in recent years. To
> compare the two methods, there two points of views need to the clarified:
>
> 1.       Granularity. It represents the extent to which a system is
> divided into smaller parts. In VBA, the brain is broken into nearly one
> million of voxels, then it is normalized before comparing with one another.
> In MRIstudio, it can superimpose the parcellation map and divided the brain
> into 150 areas, thus it has less granularity than VBA (1 million vs. 150).
> Whereas TBSS re-registers nearby voxels to the skeleton of white matter,
> reduces the granularity and increases the accuracy of registration.
>
> 2.       Anatomy. In VBA analysis, computer algorithm registers the voxels
> automatically, without considering any anatomical information. Another new
> method of Tissue-specific, smoothing-compensated (T-SPOON) can improve the
> tissue specificity in VBA method and compensation for images smoothing. TBSS
> can also apply some anatomical information, i.e., the skeleton of white
> matter, thus the registration would be better than totally automatic VBA
> method.
>
>
>
> TBSS definitely has its advantages in DTI analysis, nonetheless, it is not
> without flaw or limitation: 1.Partial volume effect still exists in TBSS
> method, and the problem may be greatly exacerbated in spatial smoothing; 2.
> Increased head motion can increase image blurring and bias FA value; 3. In
> regions of crossing tracts or junctions, TBSS may misinterpret the change of
> tracks in junction as apparently reduced FA; 4. Finally, in patients with
> apparent pathological changes, TBSS may exclude the areas from analysis.
>
>
>
> There are always advantages and disadvantages of each method in DTI
> studies. TBSS as new method, may be generally more accurate than VBA method,
> although it needs more sophisticated data projection approach in the future.
> We also need to keep in mind that DTI is based on information of water
> diffusion, it may help to screen and generate hypothesis rather than to draw
> a final conclusion.
>
>
>
>
>
>
>
>
> -------------------------------------------------------------------------------
>
>
>
> On 13 May 2010 23:44, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Good question Gao.
>>
>> Here is my thought (my personal opinion, of course);
>>
>> 1) you are comparing VBA and TBSS. These are methods to "define
>> corresponding pixels (or areas) across subjects", so that you can compare
>> pixel numbers such as FA and MD among different brains. This is called
>> "registration".
>> 2) These methods can be classified from different point of views;
>> 2-1) granularity: One extreme is to define the entire brain as one ROI.
>> You can get the whole brain volume, whole brain FA, or whole brain
>> histogram. While there is not much use of this approach, it is precise (do
>> 10 times and you get the same results) and accurate (nobody makes mistakes
>> about where is the whole brain except for some ambiguity about where you cut
>> the ROI in the brainstem). The other extreme is the pixel, which is the
>> smallest unit. This mean, you identify the corresponding pixels across
>> subjects. Once you map the entire 1 million pixels in one brain to the
>> other, it is the same as transforming one brain to the other (two brains now
>> have the same shape). This approach is called "normalization" and, of
>> course, not accurate because it is not possible to completely solve the
>> system and accurately map all 1 million pixels. VBA and TBSS are based on
>> this normalization procedure. There are methods to ameliorate this accuracy
>> issue. Usually VBA uses filters to blur the information. In my
>> understanding, TBSS "re-register" nearby pixel information to the core of
>> the white matter, which could be considered as a sort of filtering, reducing
>> the granularity and hopefully increasing the accuracy.
>> 2-2) Anatomy: When we do normalization, computer algorithm do not care
>> about anatomy. It just does whatever it thinks best to register pixels. This
>> is the pixel-based analysis. On the other hand, manual ROI is usually based
>> on anatomical information we can perceive. This is anatomy-based analysis.
>> Tractography-based analysis can also be considered as a kind of registration
>> method. We do, for example, tractography of the cortico-spinal tract in 10
>> subjects. Then we can define a group of pixels that belong to the CST and
>> compare the pixel values. In this way, we define a specific area across
>> subjects based on anatomy.
>> 3) In MriStudio, DiffeoMap does pixel-based registration just as VBA. You
>> can do VBA analysis. In addition, you can superimpose our parcellation map
>> and divide the brain into about 150 areas. In terms of granularity, it is
>> much less than VBA (more than 1 million pixels vs 150 areas). This is also a
>> conversion to pixel-based to anatomy-based analysis.
>> 4) Now going back to your question, VBA and TBSS are looking at the same
>> data with different point of view. First of all, the granularity is
>> different; TBSS reduces the information to the white matter core. Also, VBA
>> is completely pixel-based but TBSS, which is not completely anatomy-based
>> but has some anatomy-based factors by reducing the information to the core
>> of the white matter.
>> 5) In my opinion, all methods described above have advantages and
>> disadvantages. I don't think any one of them is better than the other.
>> Quantification based on location information is definitely one of the most
>> difficult problems we are all facing.
>> 6) On the other hand, your reviewer is correct, in a sense that it is
>> always important to compare different results to enrich your data and
>> interpretation. This is especially true if there is a tool widely used like
>> TBSS. However, it is not like, one method should be treated as the gold
>> standard and other approaches should give a similar result. If you compare
>> VBA and TBSS, you likely to get different results because as explained above
>> they are operating at the different granularity, precision, and accuracy.
>> MRI image anlaysis is very often a screening and hypothesis generating tool
>> rather than a tool to draw a conclusion. We are simply looking at 6MB
>> information based on water signal.
>>
>> So, in conclusion,
>>
>> > No, VBA is not out of date
>> > Yes, it is a good idea to compare results from widely used tools, but
>> any normalization-based method should not be considered as a gold standard
>> in my opinion. We just have to understand how they operate and what are
>> their advantages and disadvantages.
>>
>>   On Thu, May 13, 2010 at 8:07 AM, lion gao <gaolion at gmail.com> wrote:
>>
>>>   Dear Experts,
>>>
>>>
>>>
>>> I have one part of my thesis on DTI data analysis. The method I used is
>>> the voxel-based analysis (VBA) and I tried MRIstudio as well. One of the
>>> examiners pointed out that track-based spatial statistics (TBSS), as a state
>>> of art way, should have been considered.
>>>
>>>
>>> I am familiar with TBSS, only know that it may reduce systemic
>>> mis-registration inVBA and increasing papers published with the method. I am
>>> not sure whether:
>>> 1. VBA has become “out of date”,
>>> 2. and TBSS has become a “golden standard” for DTI data analysis.
>>>
>>> Can someone help to justify the situation or defense a little bit? Thank
>>> you very much in advance!
>>>
>>>
>>> Best wishes,
>>>
>>> Gao
>>>
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>>
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