Thanks so much, Mike. We were thinking 8-10 but I wanted to double-check just
in case there was something unusual/different you all had done with the 7T.
Best
Nina
On Mon, 10 Sep 2018, Harms, Michael wrote:
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
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