Hi there,
I have recently updated from FSL 5.0.11 to FSL 6.0. I am now running into issues when using the bet command (both from the command line and on the GUI). The program generates a bet file, however, when looking at this file it hasn't removed the skull at all despite changing any options or thresholds. I have also tried to reprocess some of the subjects I have previously processed and I am running into the same error. There is no error message but the file continues to have the full skull present with the exception of the first b0 image which is skull stripped. Is anyone else experiencing this error or know how to fix it?
Furthermore, for those that have processed on large datasets using an older version of FSL, is there any solution to keeping two versions of the software on the server? How do you go about wanting to process with newer tools despite beginning preprocessing with older versions?
Thank you!!
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