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 volume
Alternatively, you might consider mri_seg_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 mm3) 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. > > Thank you, > > Parsa > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1bL2PbUa0oBf3uE-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknDXkUAv0nG7TCvgdZGtxFpMopuSoaOG1DAd2Hcb1tVsAaDmHymRYxJ4t9yMfTNp_6Rw0B6zaYk45w86NY1Q_5DrDavKtV8snTWDbKA39DB8QOeiU6rCYHTWxfs4NRznwCDaSwzoAMgi2HIHvPl7e5Zz7ADzeIMiNT_JCukW7q9IrK8z7HIKo6d9MAkW9LGj3ryNK6ZEO3Mh5dYjdNu4fpz-YXwTL-eZygw0GeYa3ZBpMSfItMm8CiO-eTtCqR0H80wtU0tr8P9m2yDn310UhLFJmxLI9Xm5rJxk4FvoVxGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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