HCPpipeline error

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lei wei

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Nov 26, 2025, 12:42:25 PM (yesterday) Nov 26

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Hi HCP expert,

I am trying to run the HCP structural pipeline in LegacyStyleData mode, but the processing fails in the FreeSurfer step due to a missing surface file surf/lh.white.preaparc.rawavg.

From the recon-all/FreeSurferPipeline log, I see the following:

INFO: trgsubject = srcsubject

Saving target data

Computing bias field from rawavg

mri_normalize -sigma 8 -erode 1 -min_dist 1 \

-surface ../surf/lh.white.preaparc.rawavg identity.nofile \

-surface ../surf/rh.white.preaparc.rawavg identity.nofile \

rawavg.cmdc.mgz rawavg.norm.mgz

using Gaussian smoothing of bias field, sigma=8.000

eroding interior of surface 1 times

retaining nonmaximum suppressed points that are at least 1.000mm from the boundary

reading mri_src from rawavg.cmdc.mgz...

Copying mri_dst from mri_src

error: No such file or directory

error: MRISread(../surf/lh.white.preaparc.rawavg): could not open file

error: mri_normalize: could not surface ../surf/lh.white.preaparc.rawavg

However, I do see a file named white.preaparc.rawavg under the mri/ directory and the lh.white.preaparc can also be found at surf folder. I using FS 7.4.1 to run HCPpipeline and no T2w image as input.

Could you please to let me know how to resolve this error ？
Really appreciate for any help!