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--===============6353854364325824851== Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_CY4PR08MB363964F121ECD4DBD173D83EAC710CY4PR08MB3639namp_" --_000_CY4PR08MB363964F121ECD4DBD173D83EAC710CY4PR08MB3639namp_ Content-Type: text/plain; charset="iso-8859-1" MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable External Email - Use Caution = Hello Freesurfer team, I am currently working processing the volumetrics of exvivo brains, many of= which do not have a brainstem/cerebellum. It seems this often results in a subcortical alignment that isn't optimal, = and fails to create the pial/wm surface where freesurfer attempts to label = more ventral non-zero voxels as brainstem/cerebellum. Currently, I have to = manually edit the aseg.auto_noCCseg.label_intensities.mgz and aseg.presurf.= mgz to fix this. Is there a way to omit aseg labels (like the brainstem/cerebellum) from the= processing stream that I've overlooked? If not, would there be a potential= alternate solution such as creating a second atlas from the original sans = these ROIs and have the cross-sectional stream still run normally? Best, Kody Zalewski --_000_CY4PR08MB363964F121ECD4DBD173D83EAC710CY4PR08MB3639namp_ Content-Type: text/html; charset="iso-8859-1" MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable <html> <head> <meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Diso-8859-= 1"> <style type=3D"text/css" style=3D"display:none;"><!-- P {margin-top:0;margi= n-bottom:0;} --></style> </head> <body dir=3D"ltr"><p><span style=3D"padding: 3px 10px; border-radius: 5px; = color: #ffffff; font-weight: bold; display: inline-block; background-color:= #ff0000;"> External Email -= Use Caution </span></p><p><= /p> <div id=3D"divtagdefaultwrapper" style=3D"font-size:12pt;color:#000000;font= -family:Calibri,Helvetica,sans-serif;" dir=3D"ltr"> <p style=3D"margin-top:0;margin-bottom:0"></p> <div>Hello Freesurfer team, <br> <br> I am currently working processing the volumetrics of exvivo brains, many of= which do not have a brainstem/cerebellum. <br> It seems this often results in a subcortical alignment that isn't optimal, = and fails to create the pial/wm surface where freesurfer attempts to label = more ventral non-zero voxels as brainstem/cerebellum. Currently, I have to = manually edit the aseg.auto_noCCseg.label_intensities.mgz and aseg.presurf.mgz to fix this. <br> <br> Is there a way to omit aseg labels (like the brainstem/cerebellum) from the= processing stream that I've overlooked? If not, would there be a potential= alternate solution such as creating a second atlas from the original sans = these ROIs and have the cross-sectional stream still run normally? <br> <br> Best,<br> Kody Zalewski<br> </div> <br> <p></p> </div> </body> </html> --_000_CY4PR08MB363964F121ECD4DBD173D83EAC710CY4PR08MB3639namp_-- --===============6353854364325824851== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --===============6353854364325824851==--