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help > RE: v15 ART scrubbing
Apr 14, 2015 09:04 PM | Fred Uquillas
RE: v15 ART scrubbing
Thank you so much for this
Alfonso!
The patch was indeed effective : ]
Best,
Fred
Originally posted by Alfonso Nieto-Castanon:
The patch was indeed effective : ]
Best,
Fred
Originally posted by Alfonso Nieto-Castanon:
Hi Fred and
Noah,
Just for reference, when using the GUI you could simply define the desired thresholds (currently only in terms of a global-signal scan-to-scan Z-value, and a composite subject-motion signal mm-value) in the popup window that appears right before running the Preprocessing step (after you click on preprocessing, define your preprocessing steps, and click on 'ok'). If using batch commands to run your Preprocessing steps, you could also simply enter those same ART-threshold values in the field batch.New.art_thresholds in your batch structure (see help conn_batch). There is no need to change the .m files to edit these values (unless I guess if you want to define a new set of default values to be used by CONN by default for all of your users/projects), but if you want to do so you could edit the values in the file conn_setup_preproc.m (the lines at the beginning that read art_*=...)
On the other hand, Fred is right that ART allows many other options for thresholding (e.g. using separate motion and rotation thresholds) which could not yet be controlled from CONN (unless you choose to run ART in "interactive" mode, an manually adjust the options in the ART window for each subject, which can be time consuming). To fix this, I am attaching a small patch that allows you access all these additional options, both when using the CONN GUI (you will be prompted with a more complete window including all of the different ART thresholding options) as well as when using batch commands (see help conn_batch for additional info). To install this patch (this patch is for release 15a) simply unzip the attached file and copy the three .m functions to the CONN distribution folder overwriting the files with the same names there. I also added into this patch the generation of a art_screenshot.jpg file for each subject as part of the default ART output files. Let me know if everything works as expected or if you run into any issues.
Hope this helps
Alfonso
Originally posted by Fred Uquillas:
Just for reference, when using the GUI you could simply define the desired thresholds (currently only in terms of a global-signal scan-to-scan Z-value, and a composite subject-motion signal mm-value) in the popup window that appears right before running the Preprocessing step (after you click on preprocessing, define your preprocessing steps, and click on 'ok'). If using batch commands to run your Preprocessing steps, you could also simply enter those same ART-threshold values in the field batch.New.art_thresholds in your batch structure (see help conn_batch). There is no need to change the .m files to edit these values (unless I guess if you want to define a new set of default values to be used by CONN by default for all of your users/projects), but if you want to do so you could edit the values in the file conn_setup_preproc.m (the lines at the beginning that read art_*=...)
On the other hand, Fred is right that ART allows many other options for thresholding (e.g. using separate motion and rotation thresholds) which could not yet be controlled from CONN (unless you choose to run ART in "interactive" mode, an manually adjust the options in the ART window for each subject, which can be time consuming). To fix this, I am attaching a small patch that allows you access all these additional options, both when using the CONN GUI (you will be prompted with a more complete window including all of the different ART thresholding options) as well as when using batch commands (see help conn_batch for additional info). To install this patch (this patch is for release 15a) simply unzip the attached file and copy the three .m functions to the CONN distribution folder overwriting the files with the same names there. I also added into this patch the generation of a art_screenshot.jpg file for each subject as part of the default ART output files. Let me know if everything works as expected or if you run into any issues.
Hope this helps
Alfonso
Originally posted by Fred Uquillas:
I never thought of
editing the .m file. I've been trying to figure out how to get Conn
to command ART to also save a copy of the graph .jpgs. Maybe this
is how...
If you run ART on it's own via MATLAB (command: art) though, the default z-threshold is indeed 9, and translational movement threshold is 2mm. Something I just figured out is that if you run ART-based Scrubbing via the PreProcessing GUI it will save motion outliers using 'comp motion' (composite?), whereas if you run the toolbox on its own you have control over checking off the last box to also include rotational movement in your regressor files. The latter reveals a lot more outliers than the 'comp' default option but it is not automatized via the Conn GUI.
Anyway, maybe there's a patch for v.15 that will come out soon to be able to change the thresholds (maybe hopefully rotational thresholds, too) before the Art-based Scrubbing begins....
Fred
Originally posted by Noah Philip:
If you run ART on it's own via MATLAB (command: art) though, the default z-threshold is indeed 9, and translational movement threshold is 2mm. Something I just figured out is that if you run ART-based Scrubbing via the PreProcessing GUI it will save motion outliers using 'comp motion' (composite?), whereas if you run the toolbox on its own you have control over checking off the last box to also include rotational movement in your regressor files. The latter reveals a lot more outliers than the 'comp' default option but it is not automatized via the Conn GUI.
Anyway, maybe there's a patch for v.15 that will come out soon to be able to change the thresholds (maybe hopefully rotational thresholds, too) before the Art-based Scrubbing begins....
Fred
Originally posted by Noah Philip:
Just to bump up this conversation - I believe
the default in ART/Conn should be z = 3 for outlier removal, but it
remains 9, even after I edit the art.m file in the conn
folder. How might I proceed?
Threaded View
| Title | Author | Date |
|---|---|---|
| Noah Philip | Mar 24, 2015 | |
| Noah Philip | Mar 31, 2015 | |
| Fred Uquillas | Mar 31, 2015 | |
| Alfonso Nieto-Castanon | Apr 6, 2015 | |
| Fran | Oct 10, 2016 | |
| Jeff Browndyke | Oct 11, 2016 | |
| Fred Uquillas | Apr 14, 2015 | |
| Noah Philip | Apr 6, 2015 | |