What are the errors that you are facing? Can you provide more detail?
On 3/26/2024 9:12 AM, Saifullah Tumrani wrote:
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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
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