I wouldn¹t use censoring on HCP data that has been cleaned with ICA+FIX. There is a known issue with physiological noise in HCP data that has not yet been addressed in the released scans, but the current workaround is to use multi-variate methods like partial correlation.
Peace, Matt. On 8/2/16, 1:30 PM, "[email protected] on behalf of Burgess, Gregory" <[email protected] on behalf of [email protected]> wrote: >> 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. > >I¹m not sure to which existing analysis scripts you are referring. We >don¹t release analyses of individual scans. So, you should probably >include these censoring confounds as covariates in whatever preprocessing >you¹re 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 don¹t 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] >> 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 >[email protected] >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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
