External Email - Use Caution Dear Freesurfer Expert,
While the sphere can only be drawn using that Dr. Doug suggested, the sphere option would mess up. I have a further question as using this ROI to extract surface information from ?h.area and ?h.volume. I'm using the command line as below: $mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat However, due to the calculation of surface and volume, we need another input of sum file (ASCII file), how can I do that before I can run the above? Another simple question is, what is lh.volume.mgh in the group analysis folder processed by mris_proc? Is that a simple merge of all subjects lh.volume file? Why the number is between 0-10, is there any way I can put ?h.volume or ?h.area back to gain each subject's real volume or area value on that surface vertex? Thank you so much! Regards, Xiaoxu From: Na, Xiaoxu Sent: Wednesday, December 13, 2023 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Create a Binarized ROI for Surface Dear Freesurfer Expert, We would like to extract mean Cth values for each subject within a own-creaded ROI (surface defined), using freeview (for instance). Is it possible to create a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh file? (and then extract its mean Cth values for each subject)? I think this is not a new question, and it was posted somehow on https://secure-web.cisco.com/1p4y33YGPMt3Xr5IlZXBnYyxigfeQuk70cz1lkfaic6sGmC8qA5lauVhI1rT6YyYkzZwV4Nc5The50lU99NUP0P08OuZXZlGcV2awRfjyD8dnCwV-ej_DoLtv2aEl5L6H_XsKSYPlV5UQTHQOPgZ0OlzfqPWrMDLf7vEJTFgE0oIXHWTkjRWe-r_xTSUd-TnsGIxbMkTt75znip6awWwYkSDWqYBayh-gKCuDQewg8jam5eacT7xjQeIMCJ6PfiYZ6aRVvxfG53AvXI1SpeazLlp_w0DaKDZ2Z6lqz6bpU1tQe5fI97ACIq3V9v7itFjzK-EsQ3hCBgBEt6pwsZjn4A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FQuestionAnswers, and https://secure-web.cisco.com/12Y_VHmZg0jaAJhDvwanhu4ZGApCQtSL5-3ja3GQFrxICAVdi67GO2_8gR_lTnHYtHR-MwxWWNBDNvMEJa9c08yx0yD-X9H7YpltRixy_yTVNWDoEFmPbXVe8Aa7ObaVpP8hW0jDh-1XV-er4q9cb7punqN6dsMDnKqfCIjHj4acnDo_OC1hh6lPWT28HI4p229FEOm4tcYuBTHxAEZW-dOnvHLX_ez_m1JE33dEKJuGeJRSYhOIU1gN1SmQ5XS9xghPSHM1hldLDnfMElawFLYe6DgFpAfanXHSTixWUwyOi6ftUWtajsQslG1nG0QPgjVhOw7Q4dXRBtPKi1kWDoQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67677.html, but I'm still encountering questions. These commands did run, but together they didn't create a binarized mask with 1 for the sphere around the coordinates, and 0 for the other voxels. Would you recommend what I should change? Thank you so much! $mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --o delta.sm00.mgh $mris_fwhm \ --smooth-only \ --subject fsaverage \ --hemi lh \ --i delta.sm00.mgh \ --niters 10 \ --o delta.sm10.mgh $mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
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