Thank you,
Is it recommended to use the motion regressors with or without detrending on data that has been processed with the HCP preprocessing scripts? Is there a recommended cutoff for censoring time points or a recommended threshold of mean relative displacement for excluding a subject or run? I installed FIX and can implement it on my data, but I can only have it trained to data from your scanners at Wash U since I do not have enough additional data from our scanner here to train it on, so I do not feel comfortable using it on my data. Thank you, Michael ________________________________ From: Burgess, Gregory <[email protected]> Sent: Tuesday, August 2, 2016 2:30:10 PM To: Michael F.W. Dreyfuss Cc: [email protected] Subject: Re: [HCP-Users] Movement Confounds and Censoring > On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss <[email protected]> > wrote: > > Hi, I have some basic questions about the movement parameters that are put > out by the HCP preprocessing scripts. > > 1) What is the difference between Movement_Regressors_dt.txt and > Movement_Regressors.txt? I would like to use one as a confound. The Movement_Regressors.txt are the parameters computed from the motion correction algorithm. The Movement_Regressors_dt.txt is the same file put through a detrend command to remove the linear trend and mean. > > 2) What does each column in these represent? I'm assuming 6 directions of > displacement, and 3 for rotation? The 12 columns represent Displacement {x, y, z}, Rotation {x, y, z}, Backward Derivative of Displacement {x, y, z}, and Backward Derivative of Rotation {x, y, z} > > 3) What are the units in these and the other movement files in the output? > mm? voxels? The units are mm for displacements and degrees for rotations. > > 4) I would like to censor time points with too much motion in > Movement_AbsoluteRMS.txt. Is there a specific movement cutoff you recommend? > I have made a script that produces a censor file in the fsl format (i.e. > columns of all 0s with a 1 at the time point that is censored). Is there a > simple way to add that censor file into the existing analysis scripts along > with the motion as a confound? First, I would suggest using the Movement_RelativeRMS.txt file for censoring instead. The AbsoluteRMS reflects the total movement from the motion correlation registration target, which is the SBRef volume collected at the beginning of the scan. In contrast, the RelativeRMS reflects the amount of motion from the previous time point, which should be considered a more direct measurement of movement on that specific time point. I’m not sure to which existing analysis scripts you are referring. We don’t release analyses of individual scans. So, you should probably include these censoring confounds as covariates in whatever preprocessing you’re doing for the individual scans. After saying all of that, it is worth mentioning that FIX denoising: - Regresses a set of 24 motion parameters (six rigid body parameters, their backward derivatives, and the squares of those 12 columns) - Regresses noise component variance (orthogonal to signal components) from the scan-level ICA. In practice, the behavior of FIX is similar to regressing movement paremeters and voxel-specific censoring (plus other artifact cleanup). If you utilize FIX preprocessed data, you don’t need to regress motion parameters, and you might feel comfortable skipping censoring as well. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864 Email: [email protected] > > Thank you, > Michael > _______________________________________________ > HCP-Users mailing list > [email protected] > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=FMg6DAhRQHwDPdwDze2CIg4j1-kMkVc9h-XJ0PXmDWQ&s=ck-KAIP80cxbdHtG0fMXtiT8T_-4QzuQ-lNVQlPrDs8&e= ________________________________ 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
