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Dear infantFS-team,

We are a team of PhD students, who recently decided to use infantFS for the segmentation and surface extraction on our data.

We used the infant_recon_all command for preprocessing T1w sMRI scans from the Baby Connectome Project dataset. The pipeline runs without any errors, but we encountered noticeable inaccuracies in the reconstructed surfaces, especially concerning the pial surface. The white matter surface reconstruction was mostly accurate (with some exceptions), but in some cases even the segmentation fails as well, particularly in very young subjects. Even when the segmentation is accurate, the reconstruction of the pial surface fails to align correctly with the grey matter boundaries, often (if not always) in the medial temporal lobes. All scans have undergone quality control to include only those with minimal motion artefacts. The age range of the subjects analysed, spans from 0 to 4 years old. All scans were realigned and intensity-corrected using the iBEAT toolbox. We would gladly appreciate any assistance in understanding the causes of this problem and are looking forward to methods or changes that we need to follow in order to solve them. Attached you can find the script we used for the analysis of the scans in a .txt form. Please feel free to ask for any further information, details or materials regarding this issue.

Thanks a lot in advance for your time and help!

Best regards Thanos Tsigaras

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