Question about image acquisition order in HCP
李佳艺
I’ve been going through the HCP pipeline and had a quick question about the order of the scans.
In the HCP pipeline process, both structural MRI and functional MRI acquisitions include the BIAS_BC, BIAS_32CH, and fieldmap sequences. In addition, the structural images also include the AFI sequence. For MSMAll, are all of these images mandatory?
According to the reference documentation, the acquisition order is as shown in the attached figure. It looks like before the T1w and T2w scans there’s only one set of BIAS_BC and BIAS_32CH, and after the T1w/T2w scans there’s only one fieldmap collected. But when I check data in unprocessed\3T\T1w_MPR1\ and unprocessed\3T\T2w_SPC1\, I see BIAS_BC, BIAS_32CH, and fieldmap images in both folders. Also, T1w_MPR1\BIAS_BC.nii and T2w_SPC1\BIAS_BC.nii contain different voxel values. I’ve noticed something similar in unprocessed\3T\task\ as well. Could you help me understand how these separate bias/fieldmap images are generated, and why they’d be different?
Thanks a lot for your time!
Harms, Michael
The BIAS_BC scan in the T1w and T2w folders should be the same.
If you think that is not the case, please provide the specific command, and output, that you are using to compare the two.
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
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Glasser, Matthew
We should take a step back here. What are you trying to do? Acquire new data? Reprocess HCP data?
Matt.
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李佳艺
We are currently acquiring fMRI data and
plan to process it using the HCP pipelines in the future. From the
documentation, I noticed that the AFI, bias_BC,
and bias_32CH sequences mentioned for structural MRI are not
directly used in the HCP pipelines.
So, structural MRI preprocessing in the HCP pipelines
requires T1‑weighted, T2‑weighted, and fieldmap scans?(please
correct me if I’m wrong). For resting‑state and task fMRI preprocessing,
the bias_BC,bias_32CH, and BOLD_{RL,LR}_SB_SE sequences
are all required?
Thank you again for your help!
Best regards,Harms, Michael
No, the Bias scans are not required. And you probably want to acquire the fMRI as AP/PA rather than RL/LR.
Check out our HCP Lifespan protocol:
https://www.humanconnectome.org/hcp-protocols
Although we now suggest turning on Prescan Normalize on all scans.
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
From:
李佳艺 <ljy106...@gmail.com>
Date: Monday, November 10, 2025 at 10:07 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [hcp-users] Question about image acquisition order in HCP
Hi MH,
Previously, when I opened both files in MRIcroGL, I noticed different voxel values at the same location, which made me confused. However, I just double‑checked and confirmed that the two images are actually identical. It might have been an issue with the file download.
We are currently acquiring fMRI data and plan to process it using the HCP pipelines in the future. From the documentation, I noticed that the AFI, bias_BC, and bias_32CH sequences mentioned for structural MRI are not directly used in
the HCP pipelines.
So, structural MRI preprocessing in the HCP pipelines requires T1‑weighted, T2‑weighted, and fieldmap scans?(please correct me if I’m wrong). For resting‑state and task fMRI preprocessing, the bias_BC,bias_32CH,
and BOLD_{RL,LR}_SB_SE sequences are all required?
Sorry for the unnecessary trouble, and thank you again for your help!
Best,
Jiayi Li
在2025年11月10日星期一 UTC+8 23:47:03<mha...@wustl.edu> 写道：
The BIAS_BC scan in the T1w and T2w folders should be the same.
If you think that is not the case, please provide the specific command, and output, that you are using to compare the two.
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
From: 李佳艺 <ljy106...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, November 10, 2025 at 7:59 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Question about image acquisition order in HCP
Dear all,
I’ve been going through the HCP pipeline and had a quick question about the order of the scans.
In the HCP pipeline process, both structural MRI and functional MRI acquisitions include the BIAS_BC, BIAS_32CH, and fieldmap sequences. In addition, the structural images also include the AFI sequence. For MSMAll, are all of these images mandatory?
According to the reference documentation, the acquisition order is as shown in the attached figure. It looks like before the T1w and T2w scans there’s only one set of BIAS_BC and BIAS_32CH, and after the T1w/T2w scans there’s only one fieldmap collected. But when I check data in unprocessed\3T\T1w_MPR1\ and unprocessed\3T\T2w_SPC1\, I see BIAS_BC, BIAS_32CH, and fieldmap images in both folders. Also, T1w_MPR1\BIAS_BC.nii and T2w_SPC1\BIAS_BC.nii contain different voxel values. I’ve noticed something similar in unprocessed\3T\task\ as well. Could you help me understand how these separate bias/fieldmap images are generated, and why they’d be different?
Thanks a lot for your time!
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Tim Coalson
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Harms, Michael
Yes, you absolutely need SE-EPI with both polarities, or what we call in that Lifespan protocol "SpinEchoFieldMap" scans.
--
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
From:
李佳艺 <ljy106...@gmail.com>
Date: Monday, November 10, 2025 at 10:36 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Harms, Michael" <mha...@wustl.edu>, 李佳艺 <ljy106...@gmail.com>
Subject: Re: [hcp-users] Question about image acquisition order in HCP
Hi MH,
Thank you so much for your prompt reply — it has been a great help to me!!!
Sorry to bother you again, I noticed in the sequence list that, before the task and resting‑state fMRI acquisitions, there are additional BOLD_LR_SB_SE and BOLD_RL_SB_SE sequences.
The documentation states that these are used for topup distortion correction.
whether these two sequences are required for fMRI preprocessing in the HCP pipelines?
Thank you very much for your time and guidance.
Best regards,
Best，
JiayiLI
Error! Filename not specified.
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
李佳艺
Thank you so much for your prompt reply — it has been a great help to me!!!
Sorry to bother you again, I noticed in the sequence list that, before the task and resting‑state fMRI acquisitions, there are additional BOLD_LR_SB_SE and BOLD_RL_SB_SE sequences.
The documentation states that these are used for topup distortion correction.
whether these two sequences are required for fMRI preprocessing in the HCP pipelines?
Thank you very much for your time and guidance.
Best regards,
Best，
JiayiLI
李佳艺
Hi, Matt,
We’re collecting MRI data for a new task, and later on we’d like to run it through the HCP pipeline. So I want to know that for MSMAll, which scan sequences do we absolutely need to acquire?
Thanks so much for your help!
Best,
Jiayi Li
李佳艺
Hi MH,
Thank you very much for your reply! Previously, when I opened both files in MRIcroGL, I noticed different voxel values at the same location, which made me confused. However, I just double‑checked and confirmed that the two images are actually identical. It might have been an issue with the file download.
We are currently acquiring fMRI data and
plan to process it using the HCP pipelines in the future. From the
documentation, I noticed that the AFI, bias_BC,
and bias_32CH sequences mentioned for structural MRI are not
directly used in the HCP pipelines.
So, structural MRI preprocessing in the HCP pipelines
requires T1‑weighted, T2‑weighted, and fieldmap scans?(please
correct me if I’m wrong). For resting‑state and task fMRI preprocessing,
the bias_BC,bias_32CH, and BOLD_{RL,LR}_SB_SE sequences
are all required?
Sorry for the unnecessary trouble, and thank you again for your help!
Best regards,
Jiayi Li
李佳艺
Thank you very much for your reply.
Since the MRI scanner we currently use is different from the one employed in the HCP protocols, we are unable to obtain high‑resolution and high‑quality images for AFI or B1Tx sequences.
In the paper The Minimal Preprocessing Pipelines for the Human Connectome Project, within the section HCP Pipelines: Minimum Acquisition Requirements, AFI is not mentioned as part of the listed minimum requirements.
I would like to confirm whether it is acceptable to omit AFI acquisition when aiming to run MSMAll in the HCP pipelines.
Thank you very much for your time and guidance.
Best regards,