Questions on Extracting Morphological Features from ROI Masks in MNI152 Space

[Yang Hu]

Dear Experts,

I'd like to extract morphological features (thickness, area, volume) from MNI152-space ROI masks, using data pre-processed by HCP-Pipelines v5.0. The MNI152 space matches the HCP volumetric template.

My planned approach is:

1. Resample the volumetric ROI masks to the individual’s 164k fsLR surface (in MNI volume space) and save as a CIFTI dlabel file.
2. Use this dlabel file with the individual’s cortical thickness CIFTI (dscalar) to calculate mean thickness per ROI.

My questions are:

1. Is this workflow reasonable? If so:
  (1) how to resample a volumetric MNI152 ROI to a 164k surface dlabel file?
  (2) Which specific dscalar thickness file in the HCP output should I use?
  (3) How can I compute mean thickness per ROI from the dlabel and dscalar files (e.g., using wb_command)?
2. If not, what would be the recommended method?

Thank you for your help.

Best regards,
Yang Hu

[Glasser, Matthew]

You should not be using group average volume ROI masks with HCP data.  Please see Coalson et al., 2018 PNAS.

Matt.

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[Glasser, Matthew]

I don’t believe the analysis is worth doing then.

Matt.

 

From: Yang Hu <huyan...@gmail.com>
Date: Friday, January 23, 2026 at 8:45 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matthew" <glas...@wustl.edu>
Subject: Re: [hcp-users] Questions on Extracting Morphological Features from ROI Masks in MNI152 Space

 

Thank you for your reply and for the reference. I understand that using a group-level volumetric ROI mask is suboptimal, but sometimes there is no better alternative. For instance, the ROI mask is derived from a previous volume-based meta-analysis study.

[Yang Hu]

Thank you for your reply and for the reference. I understand that using a group-level volumetric ROI mask is suboptimal, but sometimes there is no better alternative. For instance, the ROI mask is derived from a previous volume-based meta-analysis study.

在2026年1月23日星期五 UTC+8 19:27:36<glas...@wustl.edu> 写道：

[Yang Hu]

Thank you for your insight. I will re-evaluate my study design accordingly.

On a separate note, it appears my replies in this thread are being automatically removed by the system for unknown reasons.

[Tim Coalson]

We don't prioritize having all posts show up immediately, some of them have to wait for a human to approve them (we try to keep the list free of spam).  Google groups doesn't show users a difference between a post "waiting for approval" and "removed intentionally".  We aren't facebook, please be patient.

Tim

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/f21dac8b-a889-4283-a84f-33315f045a21n%40humanconnectome.org.

[Yang Hu]

Thank you for the kind explanation. It's reassuring to know I didn't make a mistake.

[Elam, Jennifer]

Hi Yang,

If you join the HCP-Users list at https://groups.google.com/u/0/a/humanconnectome.org/g/hcp-users your messages are more likely to appear quickly.

Best,

Jenn

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From: Yang Hu <huyan...@gmail.com>
Sent: Friday, January 23, 2026 7:16 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: tim.c...@gmail.com <tim.c...@gmail.com>

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/ed02a164-02a1-49be-b51e-796f2328669bn%40humanconnectome.org.