You probably need to merge the files using something like paste. Peace,
Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Michael F.W. Dreyfuss" <[email protected]<mailto:[email protected]>> Date: Thursday, August 4, 2016 at 6:15 PM To: "Burgess, Gregory" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Movement Confounds and Censoring Thank you. On a practical note, if I want to include both motion regressors and time points censoring with a censor file I produce for each run how can I do that? I am refering specifically to the following chunk of code: #Create design files, model confounds if desired DIR=`pwd` cd ${FEATDir} if [ $Confound= "NONE"] ;then feat_model ${FEATDir}/design else feat_model ${FEATDir}/design ${ResultsFolder}/${LevelOnefMRIName}/${Confound} fi cd $DIR When I change that to the code below including another argument for thecensor file, the result is the same as if I added no confound (it ignores both arguments): feat_model ${FEATDir}/design ${ResultsFolder}/${LevelOnefMRIName}/${Confound} ${ResultsFolder}/${LevelOnefMRIName}/censor.txt How can I include both motion regression and censoring files in the design files using feat_model or another command? Thank you, Michael ________________________________ From: Burgess, Gregory <[email protected]<mailto:[email protected]>> Sent: Thursday, August 4, 2016 10:35:33 AM To: Michael F.W. Dreyfuss Cc: [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Movement Confounds and Censoring > On Aug 4, 2016, at 8:52 AM, Michael F.W. Dreyfuss > <[email protected]<mailto:[email protected]>> wrote: > > 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? You should perform the same filtering on your confound regressors (and task model) that you are performing on your data. So, I’d start with the original Movement_Regressors.txt. > Is there a recommended cutoff for censoring time points or a recommended > threshold of mean relative displacement for excluding a subject or run? One of the interesting difficulties with HCP data (and occasionally other MB fMRI data from other groups) is that motion parameters from MB data pick up on some source of variability that is not typically visible in motion parameters estimated from fMRI data with lower spatial and temporal resolution. So, censoring thresholds that are typical in lower resolution fMRI might result in censoring a considerable proportion of your data. You might want to look at DVARS to see if it can detect apparent motion artifact more cleanly. Either way, the best strategy is to look at your data to set your own threshold. (Look at strategies from Power, J. D., Mitra, A., Laumann, T. O., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2014). Methods to detect, characterize, and remove motion artifact in resting state fMRI. NeuroImage, 84, 320–341. https://urldefense.proofpoint.com/v2/url?u=http-3A__doi.org_10.1016_j.neuroimage.2013.08.048&d=DQIF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=rA5E466xAGA4eFveDcDcOazqcXIKVYINMcieo_qUh1o&s=W83s5PHORheYaI8ov_xC8VSiKFk3nw9qHj8Q2IvgnNg&e= ) > 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. You could consider hand categorizing the ICA components, if you feel comfortable making those judgments and you don’t have tons of data. There are also some other automated approaches such as AROMA that have become popular with folks. I have no experience with AROMA yet, but I’d imagine that it would rate spike-like ICA components as noise. --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]<mailto:[email protected]> > > Thank you, > Michael > From: Burgess, Gregory <[email protected]<mailto:[email protected]>> > Sent: Tuesday, August 2, 2016 2:30:10 PM > To: Michael F.W. Dreyfuss > Cc: [email protected]<mailto:[email protected]> > Subject: Re: [HCP-Users] Movement Confounds and Censoring > > > On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss > > <[email protected]<mailto:[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]<mailto:[email protected]> > > > > > > > > > > Thank you, > > > Michael > > > _______________________________________________ > > > HCP-Users mailing list > > > [email protected]<mailto:[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. > ________________________________ 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]<mailto:[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
