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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/1p4y33YGPMt3Xr5IlZXBnYyxigfeQuk70cz1lkfaic6sGmC..., and https://secure-web.cisco.com/12Y_VHmZg0jaAJhDvwanhu4ZGApCQtSL5-3ja3GQFrxICAV..., 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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