HCP-D rfMRI tSNR

[So-Hyeon Yoo]

 Hi,

I'm working on the HCP-D rfMRI datasets. I calculated tSNRs from the concatenated signal, it was ridiculously low. So I checked the other separated files, their means and standard deviations look OK. I also checked that the manually concatenated signal (run1AP, run1PA, run2AP, run2PA) is the same as the given file, they are not the same. Should I concatenate the signal manually?

[Glasser, Matthew]

Perhaps you can specify which files you were looking at?  Is it possible that you are using demeaned data for which TSNR is an invalid metric? 

 

I would also use fCNR rather than tSNR as a measurement of data quality.  TSNR tells you how reliable your estimate is of the mean BOLD image, which is not what you are interested in with fMRI.  fCNR is the ratio of the BOLD signal variance (e.g., the timeseries subspace spanned spatial ICA signal components) divided by the unstructured noise variance (the timeseries subspace after regressing out all ICA components) after structured artifact cleanup.

Matt.

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