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We have seen surface placement issues with FreeSurfer 7.X on HCP data as well, which is why we’ve continued to recommend folks use FreeSurfer 6.X with the HCP Pipelines for now. Overall, we’ve found that getting the surface placement right is often rather finicky and FreeSurfer version dependent and has in the past required either our developer effort or FreeSurfer developer effort or both. I have several ideas on how this could be made more robust, but it may be that mris_make_surfaces is not really set up to do things of that sort.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fredrik Magnussen fredrik.magnussen@psykologi.uio.no Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 24, 2021 at 4:49 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Differences in FLAIR assisted pial segmentation from FS6.0 to FS7.1

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Dear FreeSurfer experts,

We have processed UKB data with FLAIR assisted pial segmentation using FS7.1.

The results differs quite a lot from using FLAIR assisted pial segmentation in FS6.0.

For details please see the reported issue on the freesurfer github page: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-H8jyZpjKWbPbSPXteunZuN7BBrVhjUxtZiakU7qpRQRdF...https://secure-web.cisco.com/1BsLOtOMPefP19V4jaUIGxvB6cloD65XJYgob0S0aurJu0ta3IEnAZN0jVsHfx_1knsqnKsz9DZWc0kbv1dti4qdXg-4rk-XPtoba2GsM4NzCwfE50o-7rFAB2YR_w-BelP2wQ7IM6ZdiFaGgLX079786XnwpYGEbQ3Lt41Sl8vvQUi9WNoOLlKal7sX-lpBB86Q0-CBSUvOp6LwSazOyvMR1EZ4QyqzZfYUjoW4dQQaBSFotRqYMCVYKvlzpPbU0Yw0j59TJhtADKtB3Dhmgwg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F849. Might be related to another issue reported here (though this is T2w assisted pial segmentation): MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1M1nmgn9Ly2y8n5pthcgw-sc4hYOho93Qm1ScreoTwVFvQd...https://secure-web.cisco.com/1ZD-HjicZD5y6JRb7Rg-7byCuNf0LNbmLLvFu37e46JHBZBq5FE0IaYO4gtLYhLvWEc5cp8i4pFQ_QNYctg6hSBf-B6IhP79lIIE4Pz7jQ_sK2SjGEsjMHLECy6qKxX1BlJuRqaltVC4m_frv-vJIOKgifYMW6X9KiCdblrABCYReduMbg9nXFXWZObxchgY5Bfnc5EgwoT26qPP2Y2xFDCsJTusNL0V-XlLPmLbS68OCaAXURCxoziCQIlcCDqx-x_9KuuSvoI-D58gNRloSZg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F747.

The FS pial segmentation for UKB data is prone to include dura if only T1w data is used, so assisting with FLAIR is quite detrimental.

Best regards, Fredrik Magnussen

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