Questions about HCP-Aging PCASL acquisition parameters

[Yen-Wen Chen]

Dear experts, 

I am working on the HCP-Aging (2.0 Release) unprocessed images and I am trying to convert the data into BIDS (v1.6.0) format. 

I have some questions about the PCASL data as some required information for BIDS is not available in the corresponding json file ('HCA7467588_V1_MR_mbPCASLhr_PA' from 'imagingcollection01'). 

(1) Is 'ArterialSpinLebelingType' 'PCASL'?

(2) the 'PostLabelingDelay': from the imaging protocol ('HCP_VE11C_CMRRmb_CMRRmbPCASL_MartinosT1T2vNav_2019.01.14', which I downloaded from the Study protocol), the Postlabeling delay is "1641860 us" (= 1.641860 seconds). However, from Harms et al. (2018) Extending the HCP across ages, multiple post-labeling delays (5 PLDs: 0.2, 0.7, 1.2, 1.7, 2.2 s) were used. Which value (or array of values, if multiple PLDs) should I include in BIDS json file?

(3) 'BackgroundSuppression': no background suppression was implemented, correct?

(4) 'M0Type': the protocol (CMRR MB-EPI PCASL) suggests that "two M0 images after label/control image series were acquired, and the mean image can be used for CBF quantification". My question is that are these two M0 images contained within the '*_mbPCASLhr_PA.nii.gz'? 

(5) 'TotalAcquiredPairs': are there 45 pairs of label/control images? (the Measurements from the protocol is 90)

(6) 'LaeblingDuration': from the protocol, it is 1.5 seconds?

Any inputs would be very helpful. Thank you so much.

Best, 

Samantha

 

[Harms, Michael]

 

Hi,

We can’t really speak to how to translate the PCASL sequences into BIDS, as I don’t know the BIDS specification for ASL (e.g., how it handles the case of multiple post-label delays).

 

The protocol acquired 12, 12, 12, 20, and 30 volumes at post-labeling delays of 0.2, 0.7, 1.2, 1.7, and 2.2 sec, respectively.  Label duration of 1.5 sec.  No background suppression.

 

There are 43 label/control pairs (86 frames), followed by 2 noise images and 2 M0 images (I don’t recall the order, but it is obvious from the data).  Thus 90 frames in total.

 

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: Yen-Wen Chen <yen-we...@stonybrook.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, October 7, 2021 at 1:00 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Questions about HCP-Aging PCASL acquisition parameters

 

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[Yen-Wen Chen]

Hello Michael, 

Thank you for the response and clarification. Those information is really what I need for the moment!

Thank you.

Best, 
Sam. 

[Taylor Salo]

Apologies for resurrecting this thread, but I was hoping to get more information about the ASL scan's "noise" volumes. Are these noise volumes no-excitation-pulse volumes, like the noise scans used by NORDIC?

[Elam, Jennifer]

Hi Taylor,

I forwarded your question to Tom Kirk on the ASL team and here's his reply:

Sorry for the delayed reply, I was travelling.

 

“Noise” isn’t one of the standard pipeline outputs, so I’m not sure exactly what they are referring to. I am guessing they mean the oxford_asl / basil ‘noise_mean.nii.gz’ output file. This is produced during the model fitting process and represents the variance of white noise estimated in each voxel of the image. Note the confusing terminology: the filename noise_mean actually represents a ‘best estimate’ of the variance of the zero mean white noise.

 

Hope this helps

Tom

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project

Washington University School of Medicine

Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org

---

From: Taylor Salo <tsa...@gmail.com>
Sent: Wednesday, July 31, 2024 12:38 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Yen-Wen Chen <yen-we...@stonybrook.edu>; Harms, Michael <mha...@wustl.edu>
Subject: Re: [hcp-users] Questions about HCP-Aging PCASL acquisition parameters

 

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/03321d83-d459-42cd-93dc-51fe2d0f660en%40humanconnectome.org.

[Harms, Michael]

I think Tom was confused what Taylor was referring to, which are two “noise” (no RF) volumes acquired just before the end of the CMRR MB PCASL sequence (not anything related to the Oxford ASL pipeline output).

 

Cheers,

-MH

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

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