help > RE: CONN Pipeline: ART Implicit Mask Error?
Jan 10, 2019  02:01 PM | Alfonso Nieto-Castanon - Boston University
RE: CONN Pipeline: ART Implicit Mask Error?
Hi Jeff,

This means that ART run into a problem when creating either the art_mask_*.nii or art_mean_*.nii files. The former is an implicit mask of brain voxels that is not influenced by potential outlier scans (it is computed as the conjunction of the implicit masks across all non-outlier timepoints), and the latter is a mean-functional volume that again is not influenced by potential outlier scans (it is computed by averaging only across non-outlier timepoints). In general CONN does not use the former at all, and it only uses the latter if available (otherwise CONN defaults to using the meanfunctional.nii image that is created during the realignment preprocessing step. This means that this error is not terribly concerning (I do not believe the added robustness of using the art_mean_*.nii image over the meanfunctional.nii image will make a big difference generally, although it can really help in cases when there are really dramatic outliers) but I would really like to know the source of the error even if just for debugging purposes. If you do not mind it would be helpful if you could please re-run ART just for one individual subject but this time using the ART gui so that we can see what is causing this error. You may do so by:

1) in the Setup.Functional tab, select the 'Primary dataset' and click on 'functional tools. Apply individual-preprocessing step' (we are going to run ART on the already preprocessed data just to avoid any of your original files being overwritten)

2) in the new preprocessing window, unselect the 'All subjects' checkbox and select a single subject there, select the 'functional Outlier detection (ART-based identification of outlier scans for scrubbing)' option, and change the option that reads 'run process and import results to CONN project' to 'run process only (do not import results)' (we are doing this also to avoid CONN changing any of your current project info), and then click 'Start'

3) in the new 'functional outlier detection settings' window, select the option that reads 'edit settings interactively (ART gui)' and click on 'Ok'

and 4) in the main ART gui click on 'Save' (in the bottom right corner), and then select 'Analysis mask' and 'Mean functional' sequentially. One of these should produce an error, if you could please copy and paste the entire error message and send it to me that would be very helpful


Originally posted by Jeff Browndyke:
I was re-processing a dataset with the newest CONN version and ran across this systematic (potential?) error for all subjects:

"Warning. Error encountered during ART implicit-mask file creation. Skipping this step"

Everything else appears to work fine during the ART outlier detection process. 

Is this of concern?


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Jeff Browndyke Dec 31, 2018
RE: CONN Pipeline: ART Implicit Mask Error?
Alfonso Nieto-Castanon Jan 10, 2019
Jeff Browndyke Jan 10, 2019
Jeff Browndyke Jan 17, 2019
Alfonso Nieto-Castanon Jan 17, 2019