You can also use something likemri_segstats --seg aparc+aseg.mgz --id 1027 --mask overlay.nii.gz --sum summary.dat
you can set a threshold to the mask with --maskthresh
On 6/17/2023 7:45 AM, John Anderson wrote:
External Email - Use Caution Let's say the red spot is overlay.nii.gz 1) convert aparc+aseg from mgz to nii.gz using: mri_convert aparc+aseg.mgz aparc+aseg.nii.gz 2) create mask between overlay and the atlas using fslmaths: fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_overlap.nii.gz 3) use fslstats (or mris_cacl) to compute volume: fslstats aparc+aseg.nii.gz -k overlay_overlap.nii.gz -V this output #voxels and volumeAlternatively, you might consider mri_seg_overlap *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wW7PabrnRhUXc_r2lUdCLxnfA_3Ut8ldCl10jyleKNjKLmNnxYPpofAXJg7I4ihE3N97g1l_JcEcROS2nhvudUvFazzKGlBRfArV-mIhbdiISfFAJOZMfWjgB90oQKyxMC_gJJRwkWnB8IOny0CHVyf1DEkZg2bSsO6S0mdrfxDGePkgZUOoPQEJRpdrs9f9FBQAl3aNxZHkzTdcP94Vu-vxFxuR7XH177lhWgddopNffoUGgcKH_jLU-VJNxVdktLQWs4ItphTTI1AdpNijHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_overlap <https://secure-web.cisco.com/1yEdORqlIEup_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa8GFaC4IypTfW6sCwqLkCV8-04lx4IwpYw1bloRw_V6dP7ZHDGcAKW_GxvmcPnNpEDrGOUP0_IOqBySvJcnPNi6vhkSVi10dToaEBiERpqDFz-EnxCjEgNGIJ3XNt-k3tKuVVXCHwRVILgioT9OGbo6ypjpXFGP3ZXbaHEcno4FQfRfil7Daqyt9jtk6hu7MV49cAA-kVltRnz0XNs6FPf7MtEN0eemFGiV1vvMIp5rjRfhyA2LWaKuhK4F6Eq2uHqE_n9TYs6AsXPSvtrmL8vi3cGm-6XyMKJwBQAM1Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_overlap>On Fri, Jun 16, 2023 at 10:37 PM parsa...@student.ubc.ca <parsa...@student.ubc.ca> wrote:External Email - Use Caution Hello, Hope you are doing well. I'm new to freesurfer so I was wondering if you could help me out with something please. I'm looking for a simple way to find the size (i.e. volume in mm^3 ) of overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in an aparc+aseg file and a NIfTI volume file that can be overlayed on the aparc+aseg file. Please look at the attached file for a better visualization of what I'm describing. I'd really appreciate it if you could point me in the right direction. 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