External Email - Use Caution Ok thank you! If we conducted a study measuring brain to intracranial volume ratio, do you think that BrainVolNotVent and Etiv-only ratio would provide accurate measures? Is there another more robust way to make this calculation using FreeSurfer? We are studying brain atrophy in MCA stroke patients. I have seen studies indicating there is some bias regarding etiv but that the correlation with manual segmentations is roughly R =.8. Is the BrainVolNotVent to Etiv-only ratio a valid estimation of atrophy or are there statistical normalizations or corrections that complicate that procedure?
Thank you so much for your time. -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 tjhar...@uams.edu<mailto:tjhar...@uams.edu> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Monday, August 24, 2020 at 9:14 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] BrainSegNotVent {Disarmed} No, you need a segmentation On 8/23/2020 8:18 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg command? -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 tjhar...@uams.edu<mailto:tjhar...@uams.edu> From: <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, August 23, 2020 at 2:03 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] BrainSegNotVent Actually, that file won't be there either because it does not get created until all processing is done (not just autorecon1). You can run mri_segststats like mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default --sum subject/stats/aseg.presurf.stats Then add up all the segmentations you want to get BrainSegNotVent On 8/23/2020 11:42 AM, Douglas N. Greve wrote: Are you using v7? If so, look in subject/stats/brainvol.stats On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Hello, I am a student learning free surfer. I was able to obtain intracranial volume by running recon-all –i file.dcm –subject bert –autorecon1 and then mri_segstats --subject bert --etiv-only How can I obtain the BrainSegNotVent volume? I have tried mri_segstats --subject bert --brain-vol-from-seg however, “ERROR: must specify a segmentation volume” Can this be calculated using the data from autorecon1, or do I need to run -all? Which segmentation do I need to specify? My contact information is below, Thank you! -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 tjhar...@uams.edu<mailto:tjhar...@uams.edu> ________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMDaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=lni-DQNMfZ-oN8R6xJFbHeLbIOeuCDm_BNtoxxmTiPk&m=I3RBmsi08b81UaFeHJU3zEQRYqqdSUcG7jD4r5dhbr8&s=SSbNrPncbKhYvFBMHnGGAR7bfosOEnmO_f_Vj1At0uk&e=> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMDaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=lni-DQNMfZ-oN8R6xJFbHeLbIOeuCDm_BNtoxxmTiPk&m=I3RBmsi08b81UaFeHJU3zEQRYqqdSUcG7jD4r5dhbr8&s=SSbNrPncbKhYvFBMHnGGAR7bfosOEnmO_f_Vj1At0uk&e=> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMDaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=lni-DQNMfZ-oN8R6xJFbHeLbIOeuCDm_BNtoxxmTiPk&m=6lNsQeGlsYWKy5H0xT0IXnOUEr7d_CN3Olx_gGlcpH0&s=-P6lABwEu82r08D-MKYy9m9k0XCqCTIfmwq0o-GNZ9E&e=>
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