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I am using freesurfer to preprocess my t1w 3d Mris using autorecon1 which includes first 5 preprocessing techniques till skullstripping it worked well for 4 different datasets including ixi one from open neuro SRBPS but when i am using it for another dataset which has alsmost same configuration it’s talairach transformation fails for some samples and brain matter is removed in the final brainmask.mgz file moreover i applied autorecon-all for this dataset and even the process stopped for some showing error talaraich failed and for some samples the whole pipeline was executed without any error but in manual inspection i found brain matter removed by freesurfer kindly help me solving this problem. I later found bad skull stripping fix at this link FsTutorial/SkullStripFix_freeview - Free Surfer Wiki https://secure-web.cisco.com/1W6bcIn5Fy404rUlulLdvgZBsqq1rLSJmG1UU4wSK-ttJnEDte_j-8UbOdZbyAWxGbsnSltt5uSbWjUAYnWCyfk6YoKGWOypVyOO6Fq7Tbjfg2zFKSFazwFupik09ZRQn9DiOw-KipKyk70OGrmNDjhlHc8PjaT94sY8DLwAq_g99EjRL-uhI5FbCWuEKjjvBcWYQwN0uX9ZRFjoJEqvsVognaYjI84nWv1I8InfLai0eep0nApWU8x2cqpyiDKO_6c8Oif5TfPJ3k1v5t89WtOAdapk020sOYSVv4lpWfKh0aPPjiU7Z7C5kaMxlq-1bQ3cBRkFVn6bEOIH2uTKhrA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FSkullStripFix_freeview using some commands but i am facing errors using these command recon-all -skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip1_before
kindly look into this if you have also experience same issues or have any insight on this. A response will be appriciated.
Thanks
