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

Fri Sep 27 19:19:26 EDT 2013

Thank you Dr. Mori. Your explanation was very helpful.

About DWI intensities, I am still perplexed to why the same subject gets so
different DWI intensities, only 5 minutes apart. There must be something to
do with the machine, all else being equal.

Best regards.

2013/9/27 Susumu Mori <smoriw at gmail.com>

> I think it's happens. This is an expected range. Unless you turn off
> auto-gain setting in the second run, the scanner does automatic gain
> setting (something like automated determination of the volume of your
> stereo) and the signal intensity (equivalent of the loudness of the sound)
> varies.
> If you combine these two, the first scan with higher intensities receive
> more weighting (when both scans have corresponding b0s). If one of the
> scans lacks b0, then you have a problem.
> I thought Hangyi once tried to implement cross-scan intensity
> normalization, but not sure if it is a default setup of the current version.
> In your case, however, because you combine the two scans as one set, this
> type of cross-scan intensity normalization won't work. So you definitely
> have a problem by combining the two scans.
>
>
> On Fri, Sep 27, 2013 at 4:06 PM, Dorian P. <alb.net at gmail.com> wrote:
>
>> Average DWI for the arcuate fibers, extracted from
>>
>> Session 1 alone
>> mean DWI = 42.8095
>> mean b0 = 85.4266
>> FA= 0.5014
>>
>>
>> Session 2 alone
>> mean DWI = 54.6673
>> mean b0 = 109.7234
>> FA = 0.4830
>>
>>
>> Is it abnormal to have these differences between DTI runs? They were
>> acquired one after the other, no other MRI sequence in between.
>>
>>
>>
>> P.s. Calculations are from a subject that has both sessions complete, no
>> b0 missing.
>>
>>
>>
>> 2013/9/27 Susumu Mori <smoriw at gmail.com>
>>
>>> 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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