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

[Dorian P.]

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
>>>>>>
>>>>>> _______________________________________________
>>>>>> mristudio-users mailing list
>>>>>> mristudio-users at mristudio.org
>>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>>> Unsubscribe, send a blank email to:
>>>>>> mristudio-users-unsubscribe at mristudio.org
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> mristudio-users mailing list
>>>>> mristudio-users at mristudio.org
>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>> Unsubscribe, send a blank email to:
>>>>> mristudio-users-unsubscribe at mristudio.org
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing list
>>>> mristudio-users at mristudio.org
>>>> http://lists.mristudio.org/mailman/listinfo/
>>>> Unsubscribe, send a blank email to:
>>>> mristudio-users-unsubscribe at mristudio.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20130927/cb6052ca/attachment.html