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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
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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_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa...
On Fri, Jun 16, 2023 at 10:37 PM parsatad@student.ubc.ca < parsatad@student.ubc.ca> wrote:
External Email - Use CautionHello,
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-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknDX... 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/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS... < https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS... .
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You can also use something like mri_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:
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Let's say the red spot is overlay.nii.gz
- 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wW7PabrnRhUXc_r2lUdCLxnfA_3Ut8ldCl10jyleKNjKLm... 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 parsatad@student.ubc.ca parsatad@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. Thank you, Parsa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xiOWpsGZYLlXQenqGQmgBycvKfW9snBcrANwoB9p4JFGcp6Gdouu9gFOlPaSxepfp4IaN6pDNh1xdcEuaUL7XfhqfxsdGd2RPHgBpCVttLLElS61LfFdIKOEW6QXSBwKvd9cBwADjiRs43N3CVU_Mqal8BwxzxPUmqpQ5Bxw9uX0pI8xPiFMwkW53IiKFHSGurMzCve-e3sG8aSiXbbtlNPjKGsewuKoANP2jreP4LkZOVM-Ot81GCZemT9uLYBNO4wQIlSubUKvQdT_k07UCw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1uxZjDCVYb0-Gb4bzjARv7ZS5WZ1TywYxBWfb0oWKZF3bBpnBVmG4Uv1drVCAiQshmaScAmc5ogHyboC-W4I3Z1JQeRxhL8zEJ1w8WEy40qr9mAL4A41QqpusqtJOU5VReYkbt9bXVytp7CR1lZhD0_7cqlI1OOlXz740JbR7omjBVZ9ZG3RLm95qI-rS7eFrNkuEDEattkCmjxJ3G5l7QR2okQdT7d0tO-Hnxq4X4HrzdCSbgdFLqFjLNnNI12qnXMSYU-jBH9cnceYGT7d0Ww/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> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1uxZjDCVYb0-Gb4bzjARv7ZS5WZ1TywYxBWfb0oWKZF3bBpnBVmG4Uv1drVCAiQshmaScAmc5ogHyboC-W4I3Z1JQeRxhL8zEJ1w8WEy40qr9mAL4A41QqpusqtJOU5VReYkbt9bXVytp7CR1lZhD0_7cqlI1OOlXz740JbR7omjBVZ9ZG3RLm95qI-rS7eFrNkuEDEattkCmjxJ3G5l7QR2okQdT7d0tO-Hnxq4X4HrzdCSbgdFLqFjLNnNI12qnXMSYU-jBH9cnceYGT7d0Ww/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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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
John Anderson -
parsatad＠student.ubc.ca