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The freesurfer download and release page, https://secure-web.cisco.com/1m4Xp1On93_NmEn7Cxw8FyoPqk6laiThpewSNU4ieoINqbE... - contains the following notice, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). Results are expected to differ in the recon-all output if you run the same subject with the same freesurfer release on two different vendors operating system; likewise it can also happen across 2 different versions of the same vendors operating system.  When the OS changes the system libraries, then the floating point math output can also change. An example of files that can differ in the recon-all output for the same subject processed with the same freesurfer release across 2 different versions of the same vendors OS are listed below. - R. different: mri/aparc.a2009s+aseg.mgzdifferent: mri/aparc+aseg.mgzdifferent: mri/aparc.DKTatlas+aseg.mgzsame: mri/aseg.auto.mgzsame: mri/aseg.auto_noCCseg.mgzdifferent: mri/aseg.mgzdifferent: mri/aseg.presurf.hypos.mgzsame: mri/aseg.presurf.mgzdifferent: mri/brain.finalsurfs.mgzsame: mri/brainmask..mgzdifferent: mri/brain.mgzdifferent: mri/filled.mgzdifferent: mri/lh.ribbon.mgzsame: mri/norm.mgzsame: mri/nu.mgzsame: mri/orig.mgzsame: mri/rawavg.mgzdifferent: mri/rh.ribbon.mgzdifferent: mri/ribbon.mgzdifferent: mri/surface.defects.mgzsame: mri/T1.mgzdifferent: mri/wm.asegedit.mgzdifferent: mri/wm.mgzdifferent: mri/wmparc.mgzdifferent: mri/wm.seg.mgzdifferent: surf/lh..fsaverage.sphere.regdifferent: surf/lh.inflateddifferent: surf/lh.inflated..nofixdifferent: surf/lh.origdifferent: surf/lh.orig.nofixdifferent: surf/lh.pialdifferent: surf/lh.pial.T1different: surf/lh.qsphere.nofixdifferent: surf/lh.smoothwmdifferent: surf/lh.smoothwm.nofixdifferent: surf/lh.spheredifferent: surf/lh.sphere.regdifferent: surf/lh.whitedifferent: surf/lh..white.preaparcdifferent: surf/rh.fsaverage.sphere.regdifferent: surf/rh.inflateddifferent: surf/rh.inflated.nofixdifferent: surf/rh.origdifferent: surf/rh.orig.nofixdifferent: surf/rh.pialdifferent: surf/rh.pial.T1different: surf/rh.qsphere.nofixdifferent: surf/rh.smoothwmdifferent: surf/rh.smoothwm.nofixdifferent: surf/rh.spheredifferent: surf/rh.sphere.regdifferent: surf/rh..whitedifferent: surf/rh.white.preaparcdifferent: surf/lh.areadifferent: surf/lh.area.middifferent: surf/lh.area.pialdifferent: surf/lh.avg_curvdifferent: surf/lh.curvdifferent: surf/lh.curv.pialdifferent: surf/lh.defect_bordersdifferent: surf/lh.defect_chulldifferent: surf/lh.defect_labelsdifferent: surf/lh.inflated.Hdifferent: surf/lh.inflated.Kdifferent: surf/lh.jacobian_whitedifferent: surf/lh.smoothwm.BE.crvdifferent: surf/lh.smoothwm.C.crvdifferent: surf/lh..smoothwm.FI.crvdifferent: surf/lh.smoothwm.H.crvdifferent: surf/lh.smoothwm.K1.crvdifferent: surf/lh.smoothwm.K2.crvdifferent: surf/lh.smoothwm.K.crvdifferent: surf/lh.smoothwm.S.crvdifferent: surf/lh.sulcdifferent: surf/lh.thicknessdifferent: surf/lh.volumedifferent: surf/lh.w-g.pct.mghdifferent: surf/lh.white.Hdifferent: surf/lh.white.Kdifferent: surf/lh.white.preaparc.Hdifferent: surf/lh.white.preaparc.Kdifferent: surf/rh.areadifferent: surf/rh.area.middifferent: surf/rh.area.pialdifferent: surf/rh..avg_curvdifferent: surf/rh.curvdifferent: surf/rh.curv.pialdifferent: surf/rh.defect_bordersdifferent: surf/rh.defect_chulldifferent: surf/rh.defect_labelsdifferent: surf/rh.inflated.Hdifferent: surf/rh.inflated.Kdifferent: surf/rh.jacobian_whitedifferent: surf/rh.smoothwm.BE.crvdifferent: surf/rh.smoothwm.C.crvdifferent: surf/rh.smoothwm.FI.crvdifferent: surf/rh.smoothwm..H.crvdifferent: surf/rh.smoothwm.K1.crvdifferent: surf/rh.smoothwm.K2.crvdifferent: surf/rh.smoothwm.K.crvdifferent: surf/rh.smoothwm.S.crvdifferent: surf/rh.sulcdifferent: surf/rh.thicknessdifferent: surf/rh.volumedifferent: surf/rh.w-g..pct.mghdifferent: surf/rh.white.Hdifferent: surf/rh.white.Kdifferent: surf/rh.white.preaparc..Hdifferent: surf/rh.white.preaparc.Kdifferent: label/lh.aparc.a2009s.annotdifferent: label/lh.aparc.annotdifferent: label/lh.aparc.DKTatlas.annotdifferent: label/lh.BA_exvivo.annotdifferent: label/lh.BA_exvivo.thresh.annotdifferent: label/lh.mpm.vpnl.annotdifferent: label/rh.aparc.a2009s.annotdifferent: label/rh.aparc.annotdifferent: label/rh.aparc.DKTatlas..annotdifferent: label/rh.BA_exvivo.annotdifferent: label/rh.BA_exvivo.thresh.annotdifferent: label/rh.mpm.vpnl.annot On Nov 3, 2025, at 06:44, Felipe da Silveira Minuceli <felipe.minuceli@unifesp.br> wrote:        External Email - Use Caution        Hello, My name is Felipe and I'm a medical student from Brazil. My research involves using Freesurfer to process neuroanatomical MRIs from several individuals. I'm collaborating with a PhD student and comparing my processed images with his. We use the same version of Freesurfer (7.4.1) and the same processing command (recon-all), but different Linux-based software and computers. However, our output data is slightly different (brain segmentation volume, surface holes, WM hypointensities, and estimated total intracranial volume) I'd like to know why this is happening? Should we get the same output data, or is this correct? Can I control other variables to get the same output data?

Thank you, --  Felipe MinuceliGraduando de Medicina(11) 97483-9774 ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 que define a Política de e-mail institucional da Unifesp._______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1AU7FaE3hPm6x46WzqcypCUmynJsb3RD7QRvTHgCpH-zp9_...