External Email - Use Caution Hi, Thank you for your response. I apologize if this is a basic question, as I am new to FreeSurfer. Could you please elaborate on what overlay.lh.mgz refers to?
Shraddha ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Tuesday, December 10, 2024 11:43 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Subject: query about mri_vol2surf You don't often get email from dgr...@mgh.harvard.edu. Learn why this is important<https://secure-web.cisco.com/1Zmq86B4uFvJMf53DBMRczkute8AooQc1bZws8Cj1GQgLisrS09UOLWDQQYbmsu11TUdL_H-ynRuYxgaOzFeoxi7QvV-zXTDXWL_X8hPsHiSytyev4ZWJ7VRVurLhhF-SPyeTLn_QQWxMG5E4fCoRaT36jpftuKgbsVK8DuA58KM1ECwOxg5siDwOb1in2dCNeIpVrRaJT8udGq69eoRnN2EmjkLkpf-H5pCZUvcE1fmU0JcfA-429cFzfWS7wJ-vvBNh0vL_9V5GWOYLJFMngLsFqztLPc1BlrZVi8JCHsVwSQzxzbKM7v1iSjL2RJSnyUBg6qUCV8hnihMvPDLqhQ/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification> For mapping to the surface, each surface vertex has an xyz coordiate in anatomical space. The registration file is used to convert this into the column, row, slice in the overlay space. The value of the overlay volume at the CRS is then assigned to that vertex. In your case, the coordinate is adjusted by projecting it along the surface normal by a distance of 0.2 times the thickness at that vertex. The overlay could be trilinearlly or cubically interpolated, but you don't have that in your command line. If you want to see the input volume and the sampled points, you can do something like freeview mri/nu.mgz:overlay=overlay.mgz:reg=register.lta -f surf/lh.white:overlay=overlay.lh.mgz When viewing in the volume, select lh.white in the upper left, then go to the lower left and check the "Use overlay color" to change the surface color from yellow to the color of your overlay On 12/6/2024 4:41 PM, Pandey, Shraddha wrote: External Email - Use Caution Hello FreeSurfer Experts, I am using mri_vol2surf to map a volume onto a surface, with the registration .dat file generated via bbregister. I would like to understand how the input volume is being sampled to generate the surface and how to visualize the sampled points. mri_vol2surf --src "$input_volume" --out "$output_surface" --srcreg "$output_reg_file" --hemi lh --projfrac 0.2 Specifically, how can I display the input_volume along with the sampled points at a projfrac of 0.2 on Freeview? Thank you in advance for your help! Shraddha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1Ov2yt66WLb27zOEiTduYgm5QG9IHsRp-2fbCfUVLzeL62WRAthg80MMSUpcAULfp2ZVrvVZqFKesBGP11kPDi7SDrH_QXtXRdWXSAPj5eBNRUzIojXnpwD8CXQEmKeU8bZEkh8uza8InxBawUX_yFUXr975g7a5XO41BXpu19_2ebRyTRatJhep7PBP1UvxNUGGon39fDEXGmowXWFEIV_aatnSGUSaQmDHYnb4H24Bs9aNrAfmriPhevratob_o2gXufT8sLe4CZrpC_LufaWhYCq7vhibQdoFFCTPm4lTBmrGNBl-e7n447mQ3rGd290qt2mVsHnZOdwiKCxfoOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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