[Homer-users] SD question

[Sobanawartiny Wijeakumar]

Thanks Rob.

Indeed, ultimately our goal is to fine-tune our image reconstruction.  Further, marginal improvements in actual representation is what we expected as well. Good to have confirmation.

We wondered about ppf values too. At default, it is set to 6 in HOMER, I believe. Do you/anyone have any thoughts as to how this would need to be changed - if it indeed needs to?

Also, I am yet to run the GLM but should I expect to see similarly scaled betas and HRFs? 

Thanks again for weighing in.

S



> On Mar 3, 2015, at 2:58 AM, 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 <mailto: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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