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Paul,
Ah, this makes sense!
If I wanted to get it into native anatomical space, is it acceptable to transform the aseg.mgz file to native anatomical space (using mri_vol2volhttps://secure-web.cisco.com/1cgUDg6fc9E052dEqhYpdUmVSNSdhqk1lkJKHWA0DyYaVyIRY3wj6bfvUP4V9FmBJ-6lx_iofbytkxodAKKM1UQhhI_YE51s-IU3Lvj-8_QDh-JCh4cLkyRVID08B5Qrp9JQKwU33Adpyat9XCVh6-ioJlOEerOD6kCnKfrV6rLg3ToMQm1bpAyGioNc-l7_TDHlC93Gm3m85ElWbfRQ5ofNQ2EPwrTzsLjuw2J_vaFMyN2EABK40SCDm3KOX8io5bMP6KtUDOlDPZIDdTTeQmwwmRZUK2jn9-FKiDGiGQJB2JvaSGjy6kkbmp5xBeECRYXkBY0QHXfE4g1PYR69XYKByPQvI_rv3_iRxForpWjI/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat) and then using ' mri_segstats --subject subjid --etiv-only' to extract eTIV in this space? I know the calculations are dependent on the talairach.xfm file (as noted in your link), so I was unsure if this was an acceptable thing to do. Unfortunately, I have data that needs to be analyzed in either native anatomical space or MNI standard space, so if it is not possible to get eTIV in either of these spaces, please let me know.
Apologies for such basic questions, I am new to FreeSurfer and its functionality! Thank you again for your help.
Best Wishes, Katie
-- Katie Jobson, M.S. PhD Student | Cognitive Neuroscience Labhttps://secure-web.cisco.com/1-vVEyUz4Ck-7xz2LmR-qYVWl7z-Vypnr0P6tDSYwNivJjskF3bsBDBPI_oK6awYDcMe9zV9YkasPzjpTQbuzfDRHjQJY0nkr103hT5mJf3GZbxHWAcrMuqEvTZAjLG6vqmL51W0xu6NYU5-hGJeRckKicVcD77bV9RmARUpXMJEL68GU49A6EuqPnxA-Lxvii44eSTjljsIp_KPBTBeSIAf16Uw6qJBpGq1ldjTRono3oaZYzNPc_g2KF4zmbQ8pxGvzYyCbe5qi-YLXyWtRZwPd-S2zQDT0wauBO8naveFs7OTWjh23qF26Q_nNNICHberLdlQz2Ts8HUVQ-3OdHgoiwPsMO9gtwg0ixhVPjFk/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F Department of Psychology and Neuroscience | Temple University [cid:cbb9c020-8c58-4942-981b-bbe8abe2a3d3] ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wighton, Paul PWIGHTON@mgh.harvard.edu Sent: Thursday, June 23, 2022 6:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] aseg.stats - eTIV volume space
Hi Katie,
FreeSurfer operates mostly in "FreeSurfer Space", which is voxel resolution of 1mm^3 and sagittal orientation.
You can compare orig.mgz to the original input to see what the difference between native space and FreeSurfer Space would be.
eTIV is computed using the transformation matrix from FreeSurfer Space to MNI305 space. There is more information here about it here: https://secure-web.cisco.com/1fAv8VSclMi1E00qLOqqHaJALwYSkesj51WLpVUNlr2wiCI...https://secure-web.cisco.com/1rjjNjsPS0UFwEuRZTVV30FilUy2rpGeFY1YBMfxfzc-z8U5bpJhx3NF9dMpOImlWQjMk9AdkQoKHftziAZWcpIhHqT_U37CqZ05CZCwWlBhmwEO7bIqwZmCNsrsUSFrkPavQQEeVEHDhpZ3mdUorplftYW1d7F2XmUhT7KaepH1F1eFiuTMnxG1TBxT43rcwZ_YGwcFER68tcqASCW4LCvVF9Mu9770j9AFPdj_ml83tBQm0Uh7dN4TDxeabLWnQoZh9gkivBFkuDgnzWmCFCAz-LmtOHPfDPz5euzNM1hvnQ-M_9gb_H9hTDyZmticonejTkEUMpcKXEjo8dlHSeE4-rwyM4ZWmd8IQC7ZHLMo/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FeTIV%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C08cf3935ee5048598acd08da5568e1bc%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C637916206220826657%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DMOmpXY1C6PLZVU%252FvplRBWlmQg9EA1CdZtcQ%252Fi5PJZAo%253D%26reserved%3D0
-Paul
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Katie Rose Jobson katie.jobson@temple.edu Sent: Thursday, June 23, 2022 6:08 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aseg.stats - eTIV volume space
External Email - Use Caution
Hi FreeSurfer experts,
I apologize if this question has been addressed, but I was unable to find a definitive answer elsewhere.
I am using the aseg.stats file to extract the estimated Total Intracranial Volume (eTIV) value to be used as a correction to my anatomical data. I just want to confirm what space this data is in. I had previously assumed this data was in native anatomical space. But I read on the wiki that this statistic is calculated using the Talairach transform file (talairach.xfm), which is the conversion from MNI305 to Talairach. I just want to ensure I am correct in the assumption that this data is represented in native anatomical space.
Thank you so much for your help in this matter.
Best Wishes, Katie
-- Katie Jobson, M.S. PhD Student | Cognitive Neuroscience Labhttps://secure-web.cisco.com/1xrIuuRt0y6JHzfnoBItGiTb1DeQBt4dkc_PZLlJ5YdmZZbKsbmNYLqIXPOVhKCM_Ju4drFyPFcra2g81hz73O5XvQzu-dsk2vwl6bVTk082njT6QZaTzSBmMTa576TexzvK4aVzLLSCNzNztYQbXNVEbvtAnL83IyueX2GOHNBa4VklljJtzW2jYjAaarhAYKFJRiDh4TsrvEDpsewimF8_jUrLWhv_GUnqAAI4zy06pGpzTJdTLoeTSgi4HA_yZNaAOW8JjuXEsnyVimmxyDqpGhdIuMKvfxdp8kOwkra7O22vxBMJ2bCV9DdgouzsR9IIAcBwSXielfrn2c9qWBeuQFxa70Rdq7DdDBu0qC_w/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F15mzkkYt-HVv32ujlEOwH-7Z0bKXddWNX6mHpHztqONWIef5bhXdtvwaqeCMAqXHV4m6rr9FTXR0PdLkBaebCNtkqJdlDdUWe9Q_S9hdsGhx1v4P-OpFyduzf1UCVUgynaahq9WCAWd90ZY4iBgZ_Hq_JHbLXJhDJquBe9on-jfDhjz-fs6tHjSz0Zv4oh1gEhFQ_Qf7BnaGC-eQvOLtweSCHRmBLLN2CDX1yIRzO-7Z8pcNS6YLJKCrJvMvrvlgASKbJuGaluqeVrpj3dPumnAXN55tFeo9HqZbVtDBT3FGwjnpF-w6Brx02SzFSS-HS0ySfOjnJRbqcfZam0r5oDg%252Fhttps%25253A%25252F%25252Fsites.temple.edu%25252Fcnltu%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C08cf3935ee5048598acd08da5568e1bc%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C637916206220826657%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DNk7rPZwqVcLMpXia5%252Fz0sqA%252F%252BYBLpWuEXK3Jay12TC8%253D%26reserved%3D0 Department of Psychology and Neuroscience | Temple University [cid:dcfe96a7-bf68-4d92-8c1e-61f5814893fa]
