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Dear Freesurfer expert,
I m running infant freesurfer with the --segfile option to do segmentations. The command I use is : infant_recon_all --s bbxx --age xx --segfile <our own segmentaion file> --forceskullstrip
The results look great and the wm and pial surface align well with the segmentation file we used. However, I am wondering with this --segfile, which steps the infant_recon_all script is calling compared to those without calling the --segfile option.
in addition, with the addition segmentation file provided, we found that the wm surface aligns too well with the 'aseg' file we provided with barely extra smoothing. We are wondering if we could submit our results for you to help us check if that looks reasonable to you.
Thank you very much,
Xiaoqian