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help > RE: denoising (compcor) is shifting all correlation histogram means to zero
Mar 8, 2019 02:03 PM | Alfonso Nieto-Castanon - Boston University
RE: denoising (compcor) is shifting all correlation histogram means to zero
That is curious. It is fine if those
distributions are all approximately centered after aCompCor, but
their means/centers should not be exactly zero (as your are right
that is the hallmark of GSR). Could you please:
1) display the distribution of QC_GCOR values across subjects (in QA plots, 'distribution of subject-level QC measures') to better look at the range of center values for those distributions
and 2) please display the QM and CSF masks for one or a few subjects just to check that these are not incorrectly extending beyond their corresponding tissue classes
Also, just checking, but it is often a good idea to also include motion and other (e.g. scrubbing) parameters as part of the denoising procedure instead of just the WhiteMatter and CSF components. Any particular reason why you would prefer not to do that in your dataset? From your figures there appear to be still some considerable level of variability in the shape of the FC distributions across subjects&sessions so I was just wondering...
Best
Alfonso
Originally posted by joshm:
1) display the distribution of QC_GCOR values across subjects (in QA plots, 'distribution of subject-level QC measures') to better look at the range of center values for those distributions
and 2) please display the QM and CSF masks for one or a few subjects just to check that these are not incorrectly extending beyond their corresponding tissue classes
Also, just checking, but it is often a good idea to also include motion and other (e.g. scrubbing) parameters as part of the denoising procedure instead of just the WhiteMatter and CSF components. Any particular reason why you would prefer not to do that in your dataset? From your figures there appear to be still some considerable level of variability in the shape of the FC distributions across subjects&sessions so I was just wondering...
Best
Alfonso
Originally posted by joshm:
We are preprocessing data using other methods,
but then put the timeseries into CONN so we can do compcor on them
and subsequent analysis.
I'm attaching a screenshot from the QA of histograms before and after denoising.
Also attaching a screenshot showing denoising parameters included...
in particular, WM and CSF selected for compcor.
filter set to include 0-100 (essentially to turn it off).
linear detrending also selected.
As you can see, there are around 60 correlation distributions here. Prior to denoising, the means are on the order of 0.1. After denoising they are ALL going to zero.
Would expect this from GSR, but that is exactly what we are trying to avoid and therefore using compcor.
Please advise... this is unexpected.
Thank you.
I'm attaching a screenshot from the QA of histograms before and after denoising.
Also attaching a screenshot showing denoising parameters included...
in particular, WM and CSF selected for compcor.
filter set to include 0-100 (essentially to turn it off).
linear detrending also selected.
As you can see, there are around 60 correlation distributions here. Prior to denoising, the means are on the order of 0.1. After denoising they are ALL going to zero.
Would expect this from GSR, but that is exactly what we are trying to avoid and therefore using compcor.
Please advise... this is unexpected.
Thank you.
Threaded View
Title | Author | Date |
---|---|---|
joshm | Mar 8, 2019 | |
joshm | Mar 8, 2019 | |
Peter Coppola | Sep 20, 2019 | |
Alfonso Nieto-Castanon | Mar 8, 2019 | |
joshm | Mar 8, 2019 | |
joshm | Mar 12, 2019 | |