External Email - Use Caution Hi Freesurfer experts,
I am attempting to turn my surface-based parcellation into a segmentation file using the following command: mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask However, when I load the resulting volume using my custom LUT the ROIs get labeled to the white matter and subcortical structures leaving the grey matter unlabeled. When I examine the annotation files, they look appropriate and there isn't any overlap. Do I need to include the subcortical structures in my custom LUT to avoid this from happening or is there a better solution? Thank you! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1QkkGrc1M5CNJQjlaL6JN2C_Kh4FZGHEk5bXUEdRCEnkZGofuM17FsjaC0cgNKVyiw9zseRKNgWl7UYi7kfAZRu5vUOPJlx0s2Ia-QgtX4o_szO3739D63ABkoOt98WW7To36kJ3RGyELj3CK0t-mr__ZFDRKlYyMgt8G25IoLpVvK-TSMOqcxCmaAk6WwPqtiw0bMS6sq328dr7OygGFi5SbdSbNdRmWeipEl9x83zjjTbV0ZbWQl_nq3CIoMq7fqQJZGM0ljgbRsibrJ1UQasx4uStqpHunakdmw0kRTNM6MTMvKIkahwk208sAqQ7V/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon> Virus-free. http://secure-web.cisco.com/12C_QfaDOwg3LKh_yiXvYrqC0D4zGBhxMG0vzRqgBwZzH5moWv76SmBynqCavhx52k1BoY0EwuAUA9Tz3JxhWxBTDifYT21vJqTV-K7xU5Lg2NwJmBhYo0V6WQpIChttzNashmN_G1PMQ8tm1oZkvlwWXOUTtI63djHDCoK1scEG6-29EQQczB2479F-7hK71Nm-OVsfN5E-gxHfoTuygIaY28bqmfHcDvKhfxPXXr59-lbfp-YSJbDCfAv3KgZYQkjswRIoGRFhjJ-NEdlrhSJhX_vXZQED_OzJx0sqgkV5srCjj6rFgzfkUmDO63gwi/http%3A%2F%2Fwww.avast.com <https://secure-web.cisco.com/1tDhPrZdlS9NSF2Pe-eEm0Zojd9ScbaKYJdMT0872rwJGrh_9EMJhKwa8kdFnfCqEKffeIreGIGq7zK66tIGH7uPQhNpJFxQYtMTzxMVO5dFH9_TICZD8qopdSFWucXDIvtzKANR0O2i1FQikRSjOQ_GGN6VTxcsO3kkgX36vsLpbkHwV7FVeKf2C-6ipxbYlIyKw3xxeYAReIaUptDTHthY7JhObP6a90JAfTWm_nTGkx2g8op8mdJ3wWzUrk12fDdzuMDbAq19is2D55CEHvyNJH96fW0zJ2WaJqmqgKc-o9lwCHUZWPaDKAfswoRRo/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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