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Dear FreeSurfer,

I have modified some processing steps in NHPPipeline, but I am encountering an issue with the mris_make_surfaces command. Specifically, the pial surface generated appears correct in one half but incorrect in the other half.

I have checked the required input files (aseg, filled, wm, T1, white surface), and they all seem fine. However, the issue persists.

Here is the command I used:

VARIABLESIGMA="12" MAXTHICKNESS="-max 15" PSIGMA="-psigma 7" NSIGMA_ABOVE="-nsigma_above 12" NSIGMA_BELOW="-nsigma_below 12" MINGRAY="-min_gray_at_csf_border 10" MAXGRAY="-max_gray_at_csf_border 20"

mris_make_surfaces -variablesigma $VARIABLESIGMA $PSIGMA $MAXTHICKNESS $MINGRAY $MAXGRAY \ -white NOWRITE -aseg aseg -orig white.deformed -filled filled -wm wm \ -sdir $SubjectDIR -T1 $T1wHires $SubjectID lh -hires

I have attached the necessary input files and results for your reference. Could you please help me identify the possible cause of this issue?

Best regards, yahui