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help > RE: Importing new QC metrics as 2nd-level covariates after rerunning preprocessing?
Dec 24, 2022 12:12 AM | Alfonso Nieto-Castanon - Boston University
RE: Importing new QC metrics as 2nd-level covariates after rerunning preprocessing?
Dear Jeff,
In the Setup.Covariates (1st-level) tab, selecting the menu 'covariate tools. Compute new/derived first-level covariates' and then selecting the option 'Compute scrubbing (thresholded list-of-outliers covariate)' allows you to re-create the 1st-level scrubbing covariate applying the same or different thresholds from the ones chosen during preprocessing, and this option will also automatically re-compute the 'QC_ValidScans', 'QC_InvalidScans', 'QC_MaxMotion', 'QC_MeanMotion', 'QC_MaxGSchange', and 'QC_MeanGSchange' 2nd-level covariates with the new list of outliers (see "help conn_convertl12l1covariate" for details).
Hope this helps
Alfonso
Originally posted by Jeff Browndyke:
In the Setup.Covariates (1st-level) tab, selecting the menu 'covariate tools. Compute new/derived first-level covariates' and then selecting the option 'Compute scrubbing (thresholded list-of-outliers covariate)' allows you to re-create the 1st-level scrubbing covariate applying the same or different thresholds from the ones chosen during preprocessing, and this option will also automatically re-compute the 'QC_ValidScans', 'QC_InvalidScans', 'QC_MaxMotion', 'QC_MeanMotion', 'QC_MaxGSchange', and 'QC_MeanGSchange' 2nd-level covariates with the new list of outliers (see "help conn_convertl12l1covariate" for details).
Hope this helps
Alfonso
Originally posted by Jeff Browndyke:
We ran our preprocessing using the default
intermediate QC/ART settings, which resulted in QC second-level
covariates from the 5z/0.7mm ART thresholds. Needing to be a
bit more conservative with ART thresholding, we reran the
preprocessing routine using the conservative ART settings, which
did update the masks and regressor files. However, how do we
generate a new set of QC metrics in the second-level covariate
section to reflect the more conservative ART settings (i.e.,
QC_valid_scans for new ART threshold results)? Rerunning the
preprocessing pipeline does not automatically generate a new set of
QC second-level variables.
Thanks,
Jeff
Thanks,
Jeff
Threaded View
Title | Author | Date |
---|---|---|
Jeff Browndyke | Nov 30, 2022 | |
Alfonso Nieto-Castanon | Dec 24, 2022 | |
Jeff Browndyke | Dec 26, 2022 | |
Jeff Browndyke | Dec 26, 2022 | |
Jeff Browndyke | Dec 14, 2022 | |