[Homer-users] What happens to d and dod during processing?

[Perdue, Katherine]

Hi Adam,

It doesn’t make sense to normalize and then convert to OD. The two functions do almost exactly the same thing, like you say, except hmrIntensity2OD takes the log after normalizing and the hmrIntensityNormalized does not.

best,
Katherine

-------------
Katherine Perdue, PhD
Research Associate
Labs of Cognitive Neuroscience
Division of Developmental Medicine
Boston Children's Hospital


On Aug 5, 2016, at 4:14 PM, Adam Stone <adam.stone at gallaudet.edu<mailto:adam.stone at gallaudet.edu>> wrote:

Hi,

I just want to check my logic when building my processing stream and better understand where my data is being saved at each step.

For example, if I was to run these two steps in order:
1. hmrIntensityNormalized
2. hmrIntensity2OD
Both have the same input and output variables. Input is d (raw intensity data) and output is dod.

So it sounds like both #1 and #2 are using the same input (d), which means #2 effectively ignores #1's output and just takes the raw intensity data (d) again for conversion to OD. What I want to do is normalize it first and then convert the normalized data to OD. (If that makese sense)

Or is Homer2 smart enough to know that #2 should use the output from #1, and not just take the raw intensity data (d)?

Thanks,
Adam

--
Adam Stone
PhD Candidate, Educational Neuroscience
Petitto Brain & Language Laboratory for Neuroimaging (BL2)
Gallaudet University | http://petitto.gallaudet.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__petitto.gallaudet.edu&d=CwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=WA_1JFk0jL0vhJomc_fx9OiqPcSooSCVS1ccIEWVyPAom48e4TZPmckeX2WU3s83&m=q8YnRHaf_Fvo0pXH1JbkBcD9WEvj0JXVXM77H1STsP0&s=GgVKMj_zF_BYC1SFRvdzBB8NDNh5dBhsZ7dQL_NY4To&e=>
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