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I tried recon-all-clinical and there are two main problems
1) I ran it on a T1-MPRAGE image and it looks fine except that there are no lateral ventricles in the output. See attached.
2) I get lots of errors at the end.
I read the following note in the release notes:
*Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest version HERE https://secure-web.cisco.com/1by8vHZBkgali1lqEExldl9RRMDAvkcckApenn9NS-6rjgSKLo5qIUqnPNUWVuYYrqvir3eOqxfthWszlQKDrjt3tr2uHkrrhgVrTq4elS80ju5M0rcS9ZeaaV2rkeNGFpkdZ38977iDCM0cplU4GLNw7nhbpUvRKmAe0E2iulNqPEbWRFWtyBTTVcfQ-4I4RYaVNO_3uV-m6YlKOpz-c1cN0GmLvdHUiXO9WyKwgZwiLdVNQaZCn4DNQKVNwotbRtsPPxVOxzmb3oiKZpjnyCUNOgf5lHFQf1qh0xdTi0kHPu-2TirBonKyJbwuw3lDw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Frecon_all_clinical%2Frecon-all-clinical.sh. Development versions newer than June 15th 2023 do not have this problem.]*
I am not a linux expert, so I don't know how to download that file. If I could download it I am sure I could manage to replace it in the bin directory.
I made an attempt by clicking on the link and copying the text from my browser into a new text file. I used this to replace the supplied file, but I still get errors. Maybe I screwed up.
Michael McLaughlin, Island View, Beulah Court, Harbour Road, Dalkey Co. Dublin Ph:+353 87 688 2514
