Hi, For HCP-YA we did NOT remove any additional frames beyond the couple that Siemens automatically discards. That means that there are indeed some T1-related transient effects in that data. I'd suggest that you simply compute some time-courses averaged over the whole brain (or even better, over just CSF) and decide how many frames you want to remove.
Or, if you don't want to do that, I can say that for the HCP-Development and -Aging studies we are removing 10 frames (equivalent to 8 sec given the 0.8 s TR). Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry 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 On 9/10/18, 4:53 AM, "hcp-users-boun...@humanconnectome.org on behalf of Nina de Lacy" <hcp-users-boun...@humanconnectome.org on behalf of dela...@u.washington.edu> wrote: We are developing methods such that removal of variance using ICA would be unhelpful/disruptive to our analysis and there is a component (no pun intended) of noise identification. It would be super helpful to just know if you all saved/didn't save dummy scans and if you have an estimate of how many volumes you would advise removing for stabilization-adjustment. Thanks Nina On Sat, 8 Sep 2018, Glasser, Matthew wrote: > Unless you are developing cleaning methods you should be using the cleaned > data for any downstream analyses. Also unless you are developing > registration methods you should use the MSMAll data for best cross-subject > alignment. > > Matt. > > On 9/8/18, 8:58 AM, "Nina de Lacy" <dela...@u.washington.edu> wrote: > >> Hi Matt: >> >> Thanks for getting back to me. I probably should have specified we are >> not using the cleaned data, but the unprocessed volumetric data and >> surface mapped data for methods development. >> >> Sounds like maybe this data should have some volumes truncated? Its not >> an issue - we have automated scripts to do this - but I would just like >> to know whether its advisable and if so if you have any specific >> recommendations as to how many volumes to remove. >> >> Thanks >> Nina >> >> >> On Fri, 7 Sep 2018, Glasser, Matthew wrote: >> >>> I think you should be okay if you use the sICA+FIX cleaned data. >>> >>> Matt. >>> >>> On 9/7/18, 11:22 PM, "hcp-users-boun...@humanconnectome.org on behalf of >>> Nina de Lacy" <hcp-users-boun...@humanconnectome.org on behalf of >>> dela...@u.washington.edu> wrote: >>> >>>> Hi there: >>>> >>>> Was still hoping to get input on this question. >>>> >>>> Thanks >>>> Nina >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> Date: Thu, 30 Aug 2018 13:53:46 -0700 (PDT) >>>> From: Nina de Lacy <dela...@u.washington.edu> >>>> To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> >>>> Subject: [HCP-Users] Need to truncate dummy scans for 7T data? >>>> >>>> Hi there: >>>> >>>> For the 7T REST and MOVIE fMRI, is there a need to truncate scans from >>>> the beginning of the scan to account for stabilization? >>>> >>>> If so, does the group have a particular recommendation for how many >>>> volumes to remove? >>>> >>>> Thanks >>>> Nina >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> _______________________________________________ >>>> 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. 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 >>> >> >> This message and any attached files might contain confidential >> information protected by federal and state law. The information is >> intended only for the use of the individual(s) or entities originally >> named as addressees. The improper disclosure of such information may be >> subject to civil or criminal penalties. If this message reached you in >> error, please contact the sender and destroy this message. 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