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

[Dorian P.]

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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