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help > RE: Where are details regarding ART settings recorded
Jul 11, 2018 11:07 AM | Alfonso Nieto-Castanon - Boston University
RE: Where are details regarding ART settings recorded
Dear Rob,
Sorry about that but you are right that in old-enough versions of CONN that information was not being stored anywhere. A few options below:
1) if you run your preprocessing steps using parallelization options (either on your own computer on the background or in a distributed cluster), then you find that information in the node_*.mat files within the corresponding conn_*.qlog/#datestring# subdirectory
2) if your version creates the second-level covariates "QC_MeanMotion" and "QC_MeanGSchange", then you can also get that info from the description field of these second-level covariates, even if the log was not yet being created.
3) if your version creates a first-level covariate named 'QC_timeseries' containing the raw (unthresholded) motion and GSchange timeseries, you could then 'reverse-engineer' which threshold was used by re-creating the thresholded scrubbing covariate from the QC_timeseries covariate using different threshold values and seeing which one produces the same results as your original scrubbing covariate (to do that you may use the syntax "conn_convertl12l1covariate('scrubbing',[3 0.5],1,'QC_timeseries','new_scrubbing')" using the attached file in order to generate the new "new_scrubbing" covariate using the [3 0.5] threshold values)
If none of that works in your case, let me know which version you have and I will see if there are any other simple alternatives.
Hope this helps
Alfonso
Originally posted by Rob McCutcheon:
Sorry about that but you are right that in old-enough versions of CONN that information was not being stored anywhere. A few options below:
1) if you run your preprocessing steps using parallelization options (either on your own computer on the background or in a distributed cluster), then you find that information in the node_*.mat files within the corresponding conn_*.qlog/#datestring# subdirectory
2) if your version creates the second-level covariates "QC_MeanMotion" and "QC_MeanGSchange", then you can also get that info from the description field of these second-level covariates, even if the log was not yet being created.
3) if your version creates a first-level covariate named 'QC_timeseries' containing the raw (unthresholded) motion and GSchange timeseries, you could then 'reverse-engineer' which threshold was used by re-creating the thresholded scrubbing covariate from the QC_timeseries covariate using different threshold values and seeing which one produces the same results as your original scrubbing covariate (to do that you may use the syntax "conn_convertl12l1covariate('scrubbing',[3 0.5],1,'QC_timeseries','new_scrubbing')" using the attached file in order to generate the new "new_scrubbing" covariate using the [3 0.5] threshold values)
If none of that works in your case, let me know which version you have and I will see if there are any other simple alternatives.
Hope this helps
Alfonso
Originally posted by Rob McCutcheon:
Dear Alfonso and other CONN users,
Hopefully a simple question - where are details regarding one's chosen ART settings recorded in the CONN_x file?
It appears some files have a CONN_x.SetupPreproc.log cell array where this information is stored; but I seem to also have old projects where the "log" is not present - in these cases is there another location where this information may be available?
Many thanks
Rob
Hopefully a simple question - where are details regarding one's chosen ART settings recorded in the CONN_x file?
It appears some files have a CONN_x.SetupPreproc.log cell array where this information is stored; but I seem to also have old projects where the "log" is not present - in these cases is there another location where this information may be available?
Many thanks
Rob
Threaded View
| Title | Author | Date |
|---|---|---|
| Rob McCutcheon | Jul 9, 2018 | |
| Alfonso Nieto-Castanon | Jul 11, 2018 | |
| Rob McCutcheon | Jul 11, 2018 | |