Hi Michael, WM and CSF aren’t saved in CIFTI. Also I don’t think that you gain much by regressing those out and might even lose some. sICA+FIX will deal with movement effects but does not handle global physiological noise (which WM and CSF don’t do a good job with either). You can use temporal ICA to remove global physiological noise as will eventually be coming out in Neuroimage once they decide to make some correct proofs…
https://www.biorxiv.org/content/early/2018/03/25/193862 Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Stevens, Michael" <michael.stev...@hhchealth.org<mailto:michael.stev...@hhchealth.org>> Date: Sunday, July 22, 2018 at 9:14 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] WM and CSF signal extraction Hi folks, I apologize in advance for asking a highly specific question for which I already know there’s a better answer than what I’m asking. Long story short -- I need to know if there’s a way to reproduce the final output nifti volume file (in my pipeline case… the “clean” version that comes out of ICA-FIX) from the final CIFTI output. To explain, for space saving reasons on our Linux storage array, we truncate files we don’t think we need for CIFTI stats. Because we never need that volumetric file for anything, we’ve killed it for a couple hundred datasets on one of our R01 projects. But I probably need to quickly whip up some graph theory-style connectivity results on these data this coming week for a series of talks we’re giving next weekend. Because that volumetric file is gone in this dataset, I can’t use the lines of code from the RestingState.sh script that produces the WM.txt and CSF.txt files so I can regress out those artifact signals in each timeseries (thanks to the prior posts on the HCP listserv for pointing me to that code). So my question – Is there some useful combination of wb_command function calls that I can use to convert the final CIFTI product of the timeseries back into volume space (e.g., using the surface information that we were hopefully smart enough NOT to eradicate to save space)? I’ve already successfully worked up code that finds the WM and CSF loci via the FreeSurferWMRegLut.txt and FreeSurferCSFRegLut.txt files to extract timeseries-specific WM and CSF values. And again, I know the better way to do this probably would be to simply integrate a version of the RestingState.sh batch file into my processing pipeline and re-run things from scratch so ALL the data we need for this is produced. But my short time-frame this week prevents that… Even on our cluster, it’d take all week or longer to re-process >300 datasets. So if this is possible and someone can point me to the right commands/files, I’d appreciate it. In the end, these would just be “teaser” slides of new data. But I hate showing anything… even preliminary results… when I know the methodology isn’t as accurate as I can make it. Thanks! Mike Michael C. Stevens, Ph.D. Director, CNDLAB, Olin Neuropsychiatry Research Center Director, Child & Adolescent Research, The Institute of Living Adjunct Professor of Psychiatry, Yale University School of Medicine This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
