[Homer-users] SD question

shobana shobz_wildrose at hotmail.com
Tue Mar 3 09:56:51 EST 2015
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I see. That's very useful to know. Thanks!

I also noted that I kept calling the '6' in the HOmER code ppf but that's the DPF not ppf.  So I'll re-iterate, does anyone have any thoughts on how that DPF number changes if 3d geometry measurements are involved ? 

Thanks again!

S

Sent from my iPhone

> On Mar 3, 2015, at 03:40, Cooper, Robert <robert.cooper at ucl.ac.uk> wrote:
> 
> That's right, yes.  Though also the DPF varies with age!  These concerns are the reason why it is difficult to meaningfully compare the scale of HRFs across different arrays/ages.  Instead what tends to be compared is the HRF location, shape or latency.
> 
> 
> 
> On 3 Mar 2015, at 09:20, Wijeakumar, Sobanawartiny <sobanawartiny-wijeakumar at uiowa.edu> wrote:
> 
>> Aha! That’s another can of worms. 
>> 
>> For developmental and/or longitudinal work - it would matter the most, correct? We should be using accurate measures and not the same old SD file.
>> 
>> S
>> 
>> 
>> 
>> 
>> Sobana Wijeakumar, PhD    B-Eng
>> Postdoctoral Research Scholar
>> 
>>  E1 Seashore Hall
>> Department of Psychology
>> University of Iowa
>> Iowa City, IA 52242
>> 
>>> On Mar 3, 2015, at 3:16 AM, Cooper, Robert <robert.cooper at ucl.ac.uk> wrote:
>>> 
>>> *your probe* (!)
>>> 
>>> 
>>> 
>>> On 3 Mar 2015, at 09:14, Cooper, Robert <robert.cooper at ucl.ac.uk> wrote:
>>> 
>>>> Unless of course, you prove changes with each individual, in which case, your approach is probably the most accurate.  I don't think you need change anything else.
>>>> 
>>>> 
>>>> 
>>>> On 3 Mar 2015, at 09:01, Cooper, Robert <robert.cooper at ucl.ac.uk> wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Homer calculates the change in concentrations using a differential pathlength approach- i.e.  the mean pathlength of  photons through tissue is estimated to be DPF*SD separation.  I think I am correct in saying that adding the 3D locations to Homer will just mean your SD separation is the 3D Eulerian distance rather then the 2D equivalent.  This may be marginally more representative of the true geometry.  However, the estimates of DPF used in homer will have been estimated using a flat geometry, so it is difficult to know whether the resulting concentration changes will actually be more accurate.  The responses should look identical but will be scaled slightly differently.
>>>>> 
>>>>> 3D probe positions are useful in AtlasViewer, but unless you wish to perform image reconstruction, the advantage gained using these in Homer will be nominal.
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Rob
>>>>> 
>>>>> 
>>>>> 
>>>>> On 3 Mar 2015, at 07:57, Wijeakumar, Sobanawartiny <sobanawartiny-wijeakumar at uiowa.edu> wrote:
>>>>> 
>>>>>> Hi all
>>>>>> 
>>>>>> We are looking to fix the source and detector positions  of our SD matrix (rough 2D geometry - z dimension with all zeros created using SDGui) in our fNIRS files with actual measurements from our digitized points obtained from our Polhemus system (x,y and z dimensions - but in mm). I replaced the values in the SourcPos and DetPos arrays and ran through our processing stream. It worked without errors and I obtained similar block average waveforms as before fixing it , but the units are much smaller. 
>>>>>> 
>>>>>> Has anyone attempted to do this and had the same experience? Also, should I be changing anything else in the SD structure or any other matrix? Are there any other things I should be accounting for when I introduce 3D measurements into the calculations?
>>>>>> 
>>>>>> Any thoughts/suggestions/comments would be welcome and appreciated.
>>>>>> 
>>>>>> Thanks!
>>>>>> 
>>>>>> S
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Sobana Wijeakumar, PhD    B-Eng
>>>>>> Postdoctoral Research Scholar
>>>>>> 
>>>>>>  E1 Seashore Hall
>>>>>> Department of Psychology
>>>>>> University of Iowa
>>>>>> Iowa City, IA 52242
>>>>>> _______________________________________________
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