[Mrtrix-discussion] Is response=110 normal for white matter=400 in b0?

[Donald Tournier]

OK, that makes sense. Unfortunately it's really important to check the
voxels from the SF mask, since there are so many ways that bad ones can
creep in. As to the effect of a low response function, this will result in
correspondingly large FODs, and will mean that the default 0.1 cutoff used
for tractography will effectively be smaller than expected, allowing the
algorithm to follow more noisy and potentially spurious low-intensity FOD
peaks. Best to make sure it's properly scaled...

Cheers,
Donald.



On 28 October 2013 16:47, Dorian P. <alb.net at gmail.com> wrote:

> The single fiber mask contains voxels out of brain, from skull etc. I will
> make some attempts to better refine the DWI mask up in the processing
> pipeline.
>
> However, I still see good fiber tractography. What is the effect of low
> response function on CSD results?
>
> Yes, this is a healthy control.
>
> You help is appreciated.
> Thank you
> Dorian
>
>
> 2013/10/28 Donald Tournier <jdtournier at gmail.com>
>
>> Hi Dorian,
>>
>> That's a bit lower than I'd expect, I typically see about 3/4 of the b=0
>> intensity (I think). That's for a b-value of ~3000, I would expect it to be
>> lower than that for higher b-values. Basically, the first term in the
>> response function multiplied by ~0.28 should correspond to the mean DW
>> intensity averaged over all orientations. If that's not the case, I would
>> have a good look at your single-fibre mask (the mask from which you
>> estimate the response function), to make sure that all voxels included are
>> in sensible, single-fibre, pure WM locations. I also assume this is a
>> healthy volunteer? Otherwise T2 hyperintensity could explain this. If none
>> of this helps, maybe you can post an image of the response function, its
>> coefficients, and the b-value, SNR and number of directions of the data
>> set, just in case we can spot anything obvious from them...
>>
>> Cheers,
>>
>> Donald.
>>
>>
>>
>>
>>
>> On 25 October 2013 16:21, Dorian P. <alb.net at gmail.com> wrote:
>>
>>> Hi again MRtrix group,
>>>
>>> My processing works fine and I see the doughnut shape of the response
>>> function. On checking some quality parameters I noticed that my response
>>> function starts from ~110 while white matter values on b0 are around
>>> 350-450. Is this normal or should I look at anything to improve?
>>>
>>> This is not just a  case as I have  two HARDIs from the same subject,
>>> both around those values.
>>>
>>> Thank you.
>>>
>>> Dorian
>>> TJU
>>>
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
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>>>
>>>
>>
>>
>> --
>> *Dr J-Donald Tournier (PhD)*
>>
>> *Senior Lecturer, **Biomedical Engineering*
>> *Division of Imaging Sciences & Biomedical Engineering
>> King's College London*
>> *
>> *
>> *A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
>> Thomas' Hospital, London. SE1 7EH
>> *
>> *T: +44 (0)20 7188 7118 ext 53613*
>> *W:
>> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>> *
>>
>
>


-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*
*Division of Imaging Sciences & Biomedical Engineering
King's College London*
*
*
*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
*
*T: +44 (0)20 7188 7118 ext 53613*
*W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
*
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