How to calculate freesurfer style "MeanCurv" using HCP outputs
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Harms, Michael
Based on the completely different scales in your curvature plot, did you try just computing the mean value (with and without taking the absolute value first) of the curvature file, without the multiplication by the SA? The paper you cited might not have anything to do with how FS computes its mean curvature.
Cheers,
-MH
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Michael Harms, Ph.D.
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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:
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Date: Wednesday, August 13, 2025 at 10:31 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] How to calculate freesurfer style "MeanCurv" using HCP outputs
Dear HCP experts,
I am attempting to reconstruct FreeSurfer's statistical outputs using HCP Gifti/Cifti files for a single HCP subject. This is because I will be working with macaque data that may lack proper FreeSurfer .annot parcellation files, making this approach potentially useful for future analyses.
To test the feasibility of calculating ROI measurements in the fs_LR_32k Gifti format, I averaged the cortical thickness (CT) and summed the surface area (SA) and volume (Vol) for each ROI in the xxxx.L.aparc.32k_fs_LR.label.gii file. These results were then compared with the outputs from mris_anatomical_stats in the lh.aparc.stats file.
For CT, SA, and Vol, as shown in the figures below (x label is freesufer output), the results aligned well, consistent with a prior discussion linked here: https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/JoJcarFny7I/m/gbVjc-Z1DQAJ.
However, inconsistencies arose when analyzing MeanCurv (MC). According to FreeSurfer, MC is defined as Integrated Rectified Mean Curvature, which presumably involves taking the absolute value first and then integrating. As noted in Sebenius et al. (2023), "MC was absolute-valued, multiplied by SA and summed (thus outputting integrated rectified MC)" (10.1038/s41593-023-01376-7). Following this method, I first took the absolute value of the xxxx.Lcurvature.32k_fs_LR.shape.gii file, multiplied it by vertex-wise surface area, and then summed these values for each ROI. Surprisingly, the results showed a significant discrepancy compared to FreeSurfer's outputs.
Any insights into this inconsistency would be greatly appreciated.
Best regards,
ychuang
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11262...@qq.com
Yichun Huang
Peking University