HCP aging spin echo fieldmaps midsession

[Estephan Moana]

Hello, I'm developing a imaging protocol based on the HCP aging (Harms 2018) and have a couple of questions.

1. In the article it is stated that "A pair of spin echo images with AP and PA phase encoding...are also acquired at the beginning and middle of each scanning session...". I was under the assumption that field maps should be preferentially acquired immediately before BOLD fMRI scans to best capture head position and consequent magnetic inhomogeneities. In Harms 2018 Table 1 for session 2 shows field maps being collect before rfMRI and again before  diffusion data collection. What is the purpose of the middle session field maps?

2. For some of the task fMRI runs planned, it will be needed an interval of ~5min between them. So I am planning to collect the task fMRI of opposed phase encoding separated by other modalities such as T1w. For example: fieldmaps AP & PA, tfMRI_AP, T1w, tfMRI_PA. Do you see any problems not collecting task fMRI AP and PA scans in immediate sequence?

Thank you.

Estephan

[Harms, Michael]

Hi,

1. In “Session 2” (with the dMRI) the middle session SEFM pair is to have a back-up available for the rsfMRI scans.  In “Session 1”, the middle SEFM pair is what we would typically use for the task-fMRI scans that follow it.

 

2.  Sure, that should be fine, provided that the subject doesn’t move position dramatically.  And, as always, you want the shim in place during the SEFM pair to be the same shim that is active during the tfMRI_AP and tfMRI_PA scans.

 

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

 

From: Estephan Moana <esteph...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, December 9, 2020 at 11:41 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] HCP aging spin echo fieldmaps midsession

 

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Hello, I'm developing a imaging protocol based on the HCP aging (Harms 2018) and have a couple of questions.

 

1. In the article it is stated that "A pair of spin echo images with AP and PA phase encoding...are also acquired at the beginning and middle of each scanning session...". I was under the assumption that field maps should be preferentially acquired immediately before BOLD fMRI scans to best capture head position and consequent magnetic inhomogeneities. In Harms 2018 Table 1 for session 2 shows field maps being collect before rfMRI and again before  diffusion data collection. What is the purpose of the middle session field maps?

 

 

2. For some of the task fMRI runs planned, it will be needed an interval of ~5min between them. So I am planning to collect the task fMRI of opposed phase encoding separated by other modalities such as T1w. For example: fieldmaps AP & PA, tfMRI_AP, T1w, tfMRI_PA. Do you see any problems not collecting task fMRI AP and PA scans in immediate sequence?

 

Thank you.

 

Estephan

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[Yen-Wen Chen]

Dear experts, 

I have some questions about the SpinEchoFieldMap pairs for the corresponding functional scans. 

Corresponding to the clarification from Michael and  Harms et al., 2018 Table 1 (attached in Estephan's post above),  I am wondering if the following pairings are correct? 

(1) SpinEchoFieldMap1: for resting fMRI run 1 (both PA and AP)

(2) SpinEchoFieldMap2: for task fMRI (all three tasks, only PA)

(3) SpinEchoFieldMap3: for resting fMRI run 2 (both PA and AP)

(4) SpinEchoFieldMap4: located in Diffusion/OTHER_FILES, for resting fMRI backup 

If the above are correct, I noticed that some subjects (for example, HCA9496707) had SpinEchoFieldMap4 in their task fMRI folders (which should be SpinEchoFieldMap2?). I am wondering what is the reason for this scenario?

Thank you.

Best, 
Samantha 

[Harms, Michael]

 

As part of our internal “session building” process we check the shims on the scans.  If the shims of the SEFM’s don’t match those of the BOLD to which they are normally matched, but a later SEFM pair in the same session does match, then we associate the later SEFM pair with the BOLD.

 

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

 

 

2. For some of the task fMRI runs planned, it will be needed an interval of ~5min between them. So I am planning to collect the task fMRI of opposed phase encoding separated by other modalities such as T1w. For example: fieldmaps AP & PA, tfMRI_AP, T1w, tfMRI_PA. Do you see any problems not collecting task fMRI AP and PA scans in immediate sequence?

 

Thank you.

 

Estephan

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[Yen-Wen Chen]

Hi Michael, 

Thank you for the quick response and for the clarification. It all makes sense now. 

Best, 
Sam. 

[Yen-Wen Chen]

Sorry, I have a naive follow-up question...

If the later fieldmap pairs are used, for example, SpinEchoFieldMap4 pairs are used for task fMRI (instead of the original SpinEchoFieldMap2), is it correct to assume that all three task functional scans use the same SpinEchoFieldMap4 pairs? Or is it possible that the different SpinEchoFieldMap pairs are used for different tasks? 

What about the resting functional scans? For example, both run1 resting fMRI AP and PA scans should be expected to use the same SpinEchoFieldMap pair?

Thank you so much.

Best, 

Samantha

[Harms, Michael]

 

Hi,

In general, yes, both rfMRI runs in a pair will typically use the same SEFM pair.  Similarly, the tfMRI will generally use the same pair.  BUT, it’s not a requirement of the session building process.  If, for whatever reason (stuff happens at the scanner), one tfMRI run had shims that matched with one SEFM pair, and a following tfMRI run had shims that matched with a different SEFM pair in the same session, then different SEFMs would have been assigned to the two different tfMRI scans.

 

In short, shatever SEFM pair is associated with a given BOLD run in our released “unprocessed” directories is what got used for the processing.

Error! Filename not specified.

 

2. For some of the task fMRI runs planned, it will be needed an interval of ~5min between them. So I am planning to collect the task fMRI of opposed phase encoding separated by other modalities such as T1w. For example: fieldmaps AP & PA, tfMRI_AP, T1w, tfMRI_PA. Do you see any problems not collecting task fMRI AP and PA scans in immediate sequence?

 

Thank you.

 

Estephan

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[Yen-Wen Chen]

Thank you for the clarification! I really appreciate it.

Best, 
Sam.