Freesurfer recon-all sphere surface registration error

[Ioanna Ladopoulou]

Hello all,

I am using the HCP YA unprocessed data and running it through my own pipeline, which includes Freesurfer recon-all. A substantial proportion of my subjects are experiencing the following 2 errors:

1. Brain extraction excludes part of the occipital lobe. You can see that the intensity is higher in that part of the brain. I have tried to fix this by increasing the watershed threshold, but it has not worked so far. Here is a representative example:

2. Surface registration error - in the output sphere.reg file, the central sulcus is sometimes fragmented. Here are some examples:

Has anyone else run into this issue when using unprocessed HCP data? Are there any tips on how to reconfigure my recon-all script to potentially mitigate these issues? Here is how I am currently running recon-all for reference:

recon-all \
        -sd "$SCRATCHDIR/${SUBJECT}" \
        -s "${fs_sub}" \
        -T2 "${T2_REORIENT}" \
        -autorecon1 \
        -wsthresh 30 \
        -gcut \
        -custom-tal-atlas RLB700_atlas_as_orig \
        -parallel \
        -openmp "$OMP_NUM_THREADS"

    recon-all \
        -sd "$SCRATCHDIR/${SUBJECT}" \
        -s "${fs_sub}" \
        -T2 "${T2_REORIENT}" \
        -autorecon2 \
        -custom-tal-atlas RLB700_atlas_as_orig \
        -parallel \
        -openmp "$OMP_NUM_THREADS"

    recon-all \
        -sd "$SCRATCHDIR/${SUBJECT}" \
        -s "${fs_sub}" \
        -T2 "${T2_REORIENT}" \
        -autorecon3 \
        -custom-tal-atlas RLB700_atlas_as_orig \
        -parallel \
        -openmp "$OMP_NUM_THREADS"

Thank you in advance for any insights!

Joanna Ladopoulou

[Glasser, Matthew]

Rerunning the HCP-YA data surface generation is not recommended.  We have an explicit correction for this issue built into the HCP Pipelines.

Matt.

 

From: Ioanna Ladopoulou <jl...@usc.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, September 3, 2025 at 4:59 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Freesurfer recon-all sphere surface registration error

 

Hello all,

 

I am using the HCP YA unprocessed data and running it through my own pipeline, which includes Freesurfer recon-all. A substantial proportion of my subjects are experiencing the following 2 errors:

 

1. Brain extraction excludes part of the occipital lobe. You can see that the intensity is higher in that part of the brain. I have tried to fix this by increasing the watershed threshold, but it has not worked so far. Here is a representative example:

 

 

2. Surface registration error - in the output sphere.reg file, the central sulcus is sometimes fragmented. Here are some examples:

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