I think that will work, but there are better tools for this kind of thing. If you have 7.4, you can use mri_binarize, like mri_binarize -dilate-vertex vno surf radius outmask where vno is the center vertex, surf is the surface (eg, white), radius is the desired radius of the cicrle, and outmask is the output binary mask (eg, lh.yourcircle.mgz)
On 12/13/2023 5:25 PM, Na, Xiaoxu wrote:
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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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers https://secure-web.cisco.com/15jmZMEaxCepVMfyQImwGR_dFusKbz7ObR8zcE3AMwMwg6FQ-QTkuETE4n5SJPU_y-ULxR0ToQgr0B_LnZ-TU71vd9-uYDXh55K9eVQ23CX9kaJT60pYOX0pH6tJ69K_Ry--XuPl1mkS0Vm-sSsWKWe2iqWjc5l2Y91tqImFy3Fb1NHtO7eCCpFk8I3Th1ljqxlnFLLOdjxe5bNpse_tYAPw-_J4V3X1Y9ONydytuj8eYC1Ly6c51azXalSlz6ZF_Xa9SbBJbXCJ6wvPAnlRqcmLPaBSCkzxpYzHM8250uaUvkwrVXDetf4ppJsTfDiNl/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FQuestionAnswers, and *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67677.html https://secure-web.cisco.com/1nS4AASSkp9fTCLDzqspNVvBf35PGarlPS708pOXtzpIMD4eASchvVbZLp65PS17HOn4cF-QEOKrz967tFrvqCTjlc-sB9fVuMI1CEUkb5m657oRe3DpyjwX9zSi3drP0cPEFBtrQe-2wfm3lQVO166f3QJao-Pq2XbpVRgo5UBgmt7oKBFbiBCBvj_534G45CEE2U9KkR7EjTPPn1W6w0ur3GGywIbW1Fh8AqeJa-QPpV2hrOWwEiX9Xkh3Dh4lveR2CDXf04WAXrlgdNdDnyqPZDbW1k45Pa1C37Ew1sU8dfqpWbKwdc1z2jO2R6EHx/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
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