In general, we don’t recommend that. The HCP data were already carefully preprocessed and there needs to a be a strong justification for doing something different. A better idea would be to describe in what ways the HCP data are not currently meeting your needs and then we can see if there is a better way to get what you want.
The 7T data are pretty high temporal resolution, so slice timing correction can be omitted. Slice timing correction is not well defined in the setting of subject motion in any case.
Matt.
From: Samuel Frank <sf...@alumni.princeton.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, December 7, 2022 at 11:58 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] 7T Resting and Movies Json Sidecar Files
Hello,
My group would like to process the raw HCP 7T Resting and Movies data. In order to do so we need .json sidecar files specifying the scanning parameters. Do you happen to have these files? If not, could you provide the Slice Timing parameter.
Thank you!
Best,
Sam
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Hey Matt,
It’s only the slice timing parameters that we need. That is, the timings for each slice. The full json files aren’t necessary.
Where could we find that info?
Thanks!
Anderson
From: "Glasser, Matt" <glas...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, December 7, 2022 at 12:05 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] 7T Resting and Movies Json Sidecar Files
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Samuel, Tim,
have you seen this paper below? It might be relevant for your analysis (see also supplement)::
Gonzalez-Castillo J, Fernandez IS, Handwerker DA, Bandettini PA. “Ultra-slow fluctuations in the fourth ventricle as a marker of drowsiness” NeuroImage (2022) 259: 119424
Baris
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That’s from about 10 years ago and I haven’t seen those ideas make it into a major software package. I think I may have asked the FSL guys about it at one point. Overall, the direction folks are heading in is to just use faster imaging to address this.
Matt.
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In the interest of simply making the slice timing info public, assuming that the sequence at the time of the HCP-YA 7T data collection encoded the slice-time information correctly, this should be the slice timing info for the 7T fMRI data [obtained from the sidecar json by running a modern version of dcm2niix (“v1.0.20220720”) on a set of fMRI DICOMS from the 7T data]:
Note that similar to https://wiki.humanconnectome.org/display/PublicData/HCP+fMRI+slice-timing+acquisition+parameters, these values should only be considered accurate to 0.0025 sec.
"SliceTiming": [
0,
0.5325,
0.06,
0.59,
0.12,
0.65,
0.1775,
0.71,
0.2375,
0.7675,
0.295,
0.8275,
0.355,
0.8875,
0.415,
0.945,
0.4725,
0,
0.5325,
0.06,
0.59,
0.12,
0.65,
0.1775,
0.71,
0.2375,
0.7675,
0.295,
0.8275,
0.355,
0.8875,
0.415,
0.945,
0.4725,
0,
0.5325,
0.06,
0.59,
0.12,
0.65,
0.1775,
0.71,
0.2375,
0.7675,
0.295,
0.8275,
0.355,
0.8875,
0.415,
0.945,
0.4725,
0,
0.5325,
0.06,
0.59,
0.12,
0.65,
0.1775,
0.71,
0.2375,
0.7675,
0.295,
0.8275,
0.355,
0.8875,
0.415,
0.945,
0.4725,
0,
0.5325,
0.06,
0.59,
0.12,
0.65,
0.1775,
0.71,
0.2375,
0.7675,
0.295,
0.8275,
0.355,
0.8875,
0.415,
0.945,
0.4725 ],
--
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
From: "Glasser, Matt" <glas...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, December 8, 2022 at 4:35 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [EXTERNAL] Re: [hcp-users] 7T Resting and Movies Json Sidecar Files
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Yes, although old does not necessarily mean outdated😉
I just meant to illustrate the point that st/mc is a “combined” problem, if you want to approach it right.
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Hi Michael,
Thank you. That’s exactly what we needed.
Thank also to Matt, Tim, Baris, and Andreas for the helpful advice and references.
All the best,
Anderson
From: "Harms, Michael" <mha...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, December 8, 2022 at 5:16 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Cc: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [EXTERNAL] Re: [hcp-users] 7T Resting and Movies Json Sidecar Files
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