help > RE: QA Denoising plots do not match selected confounds
Sep 3, 2024  02:09 PM | Robert Claar
RE: QA Denoising plots do not match selected confounds

I am using CONN 22a and need to update to the most recent version to fix another issue I posted about that you recentlly answered, so perhaps the issue I describe more below will be solved from this as well.


I am specifically looking at the "QA Denoising: Distribution of functional connectivity values" plot. After I click "Done" on the "Setup" tab and CONN finishes setting up my data and brings me to the "Denoising (1st-level)" tab the default confounds present are:


White Matter (5P)


CSF (5P)


realignment (12P)


scrubbing (variable num of parameters)


Effect of task condition #1


Effect of task condition #2


and the band-pass filter is set to [0.008 0.09] Hz.


Before changing anything I click through a few of my subjects and look at their distributions of connectivity values. Then, based on my task-design and TR, I do not want to low-pass filter my data so I change the filter bounds to [0.025 Inf]. I then play around with different sets of confounds checking a few subjects connectivity distributions each time and find a set that seems to do a good job at denoising my data based on the 10 or so subjects I looked at so I want to make a QA plot to view all of the distributions of connectivity values together.


I click QA plots, create a new report, and select "QA Denoising: Distribution of functional connectivity values" and a couple other plots. I run this in parallel submitting as many jobs as I have subjects (a side note, for HPC users, it would be helpful to have the maximum possible number of jobs shown when creating QA plots as is shown when preprocessing, denoising, etc in parallel).


When the jobs complete and I go to look at the distributions of connectivity values for all my subjects, the distributions do not correspond to those generated by my selected confounds, but rather are the same distributions I saw when first landing on the "Denoising (1st-level)" tab and further when I minimize the QA report window and go back to the "Denoising (1st-level)" tab, my confounds have been reset to the default confounds that were present at the beginning.


I eventually clicked through and looked at each subjects distribution of connectivity values individually in the GUI and then ran the denoising. Afterwards as a test I recreated the QA plots and they now reflect my chosen set of confounds. Do I always need to click "Done" and actually denoise the data before creating the QA report and the corresponding plots? I figured I wouldn't need to since the individual distributions of connectivity values plots are updated automatically as you select new confounds in the "Denoising (1st-level)" tab.

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TitleAuthorDate
Robert Claar Sep 1, 2024
Alfonso Nieto-Castanon Sep 1, 2024
RE: QA Denoising plots do not match selected confounds
Robert Claar Sep 3, 2024
Alfonso Nieto-Castanon Sep 3, 2024
Robert Claar Sep 4, 2024