Re: [hcp-users] 7T Resting and Movies Json Sidecar Files

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Glasser, Matt

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Dec 7, 2022, 1:04:45 PM12/7/22
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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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Anderson Winkler

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Dec 7, 2022, 1:11:59 PM12/7/22
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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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Tim Coalson

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Dec 7, 2022, 6:22:32 PM12/7/22
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As I understand it, the fast 7T data means that slice timing is negligible when considered against the BOLD response curve, and in particular, motion is more "sudden" than the BOLD response, so using slice timing before motion correction therefore hurts your motion correction significantly more than it helps with timing.  After motion correction resampling (which in our case includes the rigid alignment and MNINonLinear warp), the correspondence between voxels and slice timings is lost, as every voxel is primarily a mix of two timings after the resampling (with the mixing dependent on what frame you are in, due to motion, and complicated by cubic interpolation being slightly sensitive to further slices in a nontrivial fashion), so even attempting to use this information after the fact seems problematic also.  What are you planning to do with the slice timing information?

Tim


Demiral, Sukru (NIH/NIAAA) [E]

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Dec 8, 2022, 1:13:15 PM12/8/22
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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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Andreas Bartsch

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Dec 8, 2022, 5:04:33 PM12/8/22
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Also see this:

·         DOI: 

·         10.1109/TMI.2011.2131152

Glasser, Matt

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Dec 8, 2022, 5:35:38 PM12/8/22
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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.

Harms, Michael

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Dec 8, 2022, 6:16:24 PM12/8/22
to hcp-...@humanconnectome.org, Harms, Michael

 

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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Andreas Bartsch

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Dec 9, 2022, 6:48:14 AM12/9/22
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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.

Anderson Winkler

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Dec 12, 2022, 12:26:34 PM12/12/22
to hcp-...@humanconnectome.org, Samuel Frank

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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