Hi Matt, I'd actually already seen the preprint in bioxiv.org. Given how strongly we like ICA-based solutions for things, I'm looking forward to being able to implement that approach in a standard way in our processing pipeline. My problem was more immediate - I'd like, if possible, do produce data that fit the "vague consensus" that graph theory-using neuroimagers have tentatively reached over the past few years as the result of lots of work by Power, Satterthwaite and the rest of the bunch who've tackled the daunting problem of comparing various combinations of preprocessing. I sit far closer to your position... I've always thought that ICA could be tweaked in ways that probably would do a better job of identifying and cleaning physiological and/or other types of structured noise.
But my issue is just more time-sensitive. Sure, I could whip up a simple cross-correlation of our timeseries data WITHOUT regressing WM and CSF. And what I have in mind is literally, just a teaser for some talks this weekend at a small, topically-focused conference. And if I were a bit more savvy with HCP tools, I'd know if it were possible to re-create that volume-based file on my own. I've already done the WM and CSF regression from the *.nii files on other GT-focused analyses using code I extracted from the RestingState.sh script. (I know WM and CSF isn't saved in CIFTI). My problem is simply I clobbered the corresponding volume-based *.nii for space-saving reasons, so I can't pull the relevant FS-labled WM and CSF values out. I'm wondering if this can be done. If not, I won't waste any more thought on it. Again, this is not crucial by any means... It's just if I'm going to do something that I already know is a bit sub-optimal, I'd like it to be "the least sub-optimal" I can possibly do in the timeframe I have available. In this case, I just have a couple of days to assemble some nice preliminary results. Best, Mike From: Glasser, Matthew [mailto:[email protected]] Sent: Sunday, July 22, 2018 10:22 AM To: Stevens, Michael; [email protected] Subject: Re: [HCP-Users] WM and CSF signal extraction This is an email from an external source. USE CAUTION opening attachments or links from unknown senders. 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_early_2018_03_25_193862&d=DwMF-g&c=e_HtEeZEQXP5NUOb33qoTj0AVvRFBS9_rhBTQcfkWoA&r=golSXqwzwyESse15ixCMA3FkCV08C4TvBJ1P6uKO0nE&m=sdiQwdVLc3DEBFKYQfH4nhD128O9fuXHMQkHTosYA6c&s=5vMtwHSGwIE0-NtN4tkLq5DfBj0_SjOJkxT6HappiaY&e=> Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Stevens, Michael" <[email protected]<mailto:[email protected]>> Date: Sunday, July 22, 2018 at 9:14 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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. 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