[Mristudio-users] Why deleting b0 from one of the runs increases FA a lot.

[Susumu Mori]

Then I believe the two sets have intensity differences by 10-20%.
Create the sum of all DWIs from the two scans and compare the intensity.


On Fri, Sep 27, 2013 at 3:27 PM, Dorian P. <alb.net at gmail.com> wrote:

> MD seem to go down for the partial dataset:
>
> Trace:
> 2 DTI runs (normal) = 2.528e-003
> 2 DTI runs (exclude 1 b0) = 2.061e-003
> 1 DTI run (normal) = 2.493e-003
>
> Same ROIs were used to extract the fasciculus in each case.
>
>
> 2013/9/27 Susumu Mori <smoriw at gmail.com>
>
>> how about MD?
>> Maybe intensities of two scans were different.
>>
>>
>> On Fri, Sep 27, 2013 at 2:56 PM, Dorian P. <alb.net at gmail.com> wrote:
>>
>>> Hi Dr. Mori
>>>
>>> That was my strategy. I  combined the two runs, b0+32DWI+32DWI. This was
>>> done of course after registration, so that I could use the new gradient
>>> table. Images were saved in raw format, and loaded back with the new
>>> gradient table.
>>>
>>> I tried both using all images with gradient 100, 100, 100 for the bad b0
>>> or completely deleting the bad b0 (and the corresponding gradient line).
>>> Either way FA goes up a lot for the same measured tract.
>>>
>>> Here are some more tests on left arcuate from a good subject with 2 DTI
>>> runs. Values are FA:
>>> 2 DTI runs (normal) = 0.489
>>> 2 DTI runs (exclude 1 b0) = 0.55
>>> 1 DTI run (normal) = 0.499
>>>
>>> It seems that excluding one b0 is much worse than excluding the whole
>>> DTI run. In other words, adding DWI images from a sequence that doesn't
>>> have its own b0 may invalidate the findings. If seems that a set of DWI
>>> images without a b0 acquired during the same sequence is not useful to to
>>> include in DTI calculation.
>>>
>>> Does this make sense?
>>>
>>> Dorian
>>>
>>>
>>>
>>> 2013/9/27 Susumu Mori <smoriw at gmail.com>
>>>
>>>> Do you mean, you used different gradient tables for different runs?
>>>> I wonder if the gradient table and images are not matched for a part of
>>>> data.
>>>> Suppose you have 1 b0 + 12 DWIs x 2 runs and you lost one b0 in the
>>>> second run.
>>>> The only way to analyze this data, I can think of, is, combine the two
>>>> runs as 1 b0 + 12 DWIs + 12 DWIs and crate one 25-element gradient table.
>>>>
>>>> In general, if you have less data, you have lower SNR and FA goes up
>>>> but I doubt if the loss of one b0 could cause such a large FA increase.
>>>>
>>>>
>>>> On Fri, Sep 27, 2013 at 10:38 AM, Dorian P. <alb.net at gmail.com> wrote:
>>>>
>>>>> Dear developers and Dr. Mori,
>>>>>
>>>>> I am comparing FA for some tracts at two time points. At each time
>>>>> point I acquire 2-3 DTI runs to increase SNR. However, the scanner has
>>>>> malfunctioned for one of the runs in one subject. As a result the B0 image
>>>>> is not saved, but all other DWIs are there. So, I set the collapsed B0 to
>>>>> gradient 100, 100, 100 and align all DWIs to the only B0 available. For
>>>>> some results, the resulting FA is increased a lot.
>>>>>
>>>>> I tried the same procedure with another subject, when I set one of the
>>>>> B0 to gradient 100, 100, 100, the resulting FA of the tract goes up from
>>>>> 0.51 to 0.62.
>>>>>
>>>>> Is there any explanation why this is happening, and whether I should
>>>>> delete completely the collapsed B0 instead of setting it to 100, 100, 100?
>>>>>
>>>>> Thank you.
>>>>> Dorian
>>>>> TJU
>>>>>
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>>>>
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