Re: [HCP-Users] Phase-encoding-direction-dependent (LR, RL) EVs files, which ones to use in first level GLM ?

[Harms, Michael]

When you concatenate two runs, the subsequent analysis is likely assuming that you are providing it a continuous time series, which it was not.  The assumption underlying the temporal autocorrelation estimate (and temporal filtering, if applied) is that the data is a continuous time series.  Now, one might argue that the impact of ignoring the discontinuity with concatenated data is quite possibly minimal -- I don't know if anyone has empirically studied or modeled that.  But why not just use the "standard" approach of combining the 2 runs in a fixed-effects, 2nd level, within subject analysis, so that you don't have to worry about the issue.    Users should know that is in fact what we have done to generate the individual subject task fMRI data that was just released as part of the HCP Q3 release. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <Glasser>, Matt Glasser <glass...@wusm.wustl.edu> Date: Tuesday, October 1, 2013 2:31 PM To: "Harms, Michael" <mha...@wustl.edu>, "Yan, Shulin" <shu.ya...@imperial.ac.uk>, Elvis Dohmatob <gmd...@gmail.com>, "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] Phase-encoding-direction-dependent (LR, RL) EVs files, which ones to use in first level GLM ? That's what I thought, but can you explain exactly why Mike? Thanks, Matt. From: <Harms>, Michael <mha...@wustl.edu> Date: Tuesday, October 1, 2013 2:30 PM To: "Yan, Shulin" <shu.ya...@imperial.ac.uk>, Matt Glasser <glass...@wusm.wustl.edu>, Elvis Dohmatob <gmd...@gmail.com>, "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] Phase-encoding-direction-dependent (LR, RL) EVs files, which ones to use in first level GLM ? Just to follow-up on what Matt said, concatenating the two runs would NOT be the way that we would recommend to process/combine the two runs per task. Best, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <Yan>, Shulin <shu.ya...@imperial.ac.uk> Date: Tuesday, October 1, 2013 2:25 PM To: Matt Glasser <glass...@wusm.wustl.edu>, Elvis Dohmatob <gmd...@gmail.com>, "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] Phase-encoding-direction-dependent (LR, RL) EVs files, which ones to use in first level GLM ? Hey DED, I just did the work. I directly combined the two data  say, _RL followed _LR. Then, you remain the EVs file of _LR, and add (232*0.72s) to the time in _RL's EVs file.  From:hcp-users-boun...@humanconnectome.org [hcp-users-boun...@humanconnectome.org] on behalf of Glasser, Matthew [glass...@wusm.wustl.edu] Sent: 01 October 2013 20:02 To: Elvis Dohmatob; HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Phase-encoding-direction-dependent (LR, RL) EVs files, which ones to use in first level GLM ? I'm not sure I understand what you are trying to do.  Are you sure you don't just want to use the individual subject task fMRI data we've already just released?   I don't think there is any way you can combine the _LR and _RL data in a first level analysis.  You need to combine them in the level 2 analysis (which uses flameo not film_gls). Peace, Matt. From: Elvis Dohmatob <gmd...@gmail.com> Date: Tuesday, October 1, 2013 1:58 PM To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: [HCP-Users] Phase-encoding-direction-dependent (LR, RL) EVs files, which ones to use in first level GLM ? Hi all, I'm trying to run first level (single-subject) GLM on task fMRI HCP data.  But I'm unsure on how to use the timing info. Example: subject 100307, MOTOR I have stimulus timing info (cue.txt , lf.txt , lh.txt, rf.txt, rh.txt, Sync.txt, t.txt) in both 100307/tfMRI_MOTOR/unprocessed/3T/tfMRI_MOTOR_LR/LINKED_DATA/EPRIME/EVs/ and 100307/tfMRI_MOTOR/unprocessed/3T/tfMRI_MOTOR_RL/LINKED_DATA/EPRIME/EVs/, but the contents of the corresponding files in both directions vary (for example, the contents of 100307/tfMRI_MOTOR/unprocessed/3T/tfMRI_MOTOR_LR/LINKED_DATA/EPRIME/EVs/lf.txt are different from 100307/tfMRI_MOTOR/unprocessed/3T/tfMRI_MOTOR_RL/LINKED_DATA/EPRIME/EVs/lf.txt). How am I to combine/merge these phase-encoding-direction-dependent EVs in my GLM ? N.B.: During the 'topup' step of my preprocessing pipeline, I already 'combined' the _LR and _RL fMRI data to produce a single 4D film Thanks in advance for your help. -- DED _______________________________________________ HCP-Users mailing list 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. 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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