[Freesurfer] manual editting not implemented
Hi, I did manual editting for lateral ventricles, fornix, basal ganglia, optic nerve, as illustrated in the cortical reconstruction tutorial, for both left and right hemispheres, and DID save them in the "wm" volume. Then I ran "create surface", but nothing is changed. What could have been wrong? Comments are appreciated. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] manual editting not implemented
hi Nam- please refrain from using the csurf interface to create surfaces. instead, run through the command line: recon-all -stage2 -subjid this will create a log file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) include this with your email so we can better assist you with your difficulties. thanks, brian On Fri, 14 Jan 2005, Joongnam Yang wrote: Hi, I did manual editting for lateral ventricles, fornix, basal ganglia, optic nerve, as illustrated in the cortical reconstruction tutorial, for both left and right hemispheres, and DID save them in the "wm" volume. Then I ran "create surface", but nothing is changed. What could have been wrong? Comments are appreciated. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] manual editting not implemented
Thanks Brian, Does that mean csurf interface is useless for "creating surfaces" to implement the editting of major topological defects? Nam. >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 01/14/05 3:22 PM >>> hi Nam- please refrain from using the csurf interface to create surfaces. instead, run through the command line: recon-all -stage2 -subjid this will create a log file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) include this with your email so we can better assist you with your difficulties. thanks, brian On Fri, 14 Jan 2005, Joongnam Yang wrote: > Hi, > > I did manual editting for lateral ventricles, fornix, basal ganglia, optic > nerve, > as illustrated in the cortical reconstruction tutorial, for both left and > right hemispheres, and DID save them in the "wm" volume. > Then I ran "create surface", but nothing is changed. > > What could have been wrong? > > Comments are appreciated. > Nam. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] manual editting not implemented
It isn't useless but being a GUI it is less stable, and the command line outputs a recon-all.log, at least the tail line of which you should include with any enquiries to the freesurfer list, otherwise it is sometimes difficult to say what caused an undesirable freesurfer result. On Fri, 14 Jan 2005, Joongnam Yang wrote: > Thanks Brian, > Does that mean csurf interface is useless for "creating surfaces" to > implement > the editting of major topological defects? > > Nam. > > >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 01/14/05 3:22 PM >>> > hi Nam- > > please refrain from using the csurf interface to create surfaces. > instead, run through the command line: > recon-all -stage2 -subjid > > this will create a log > file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) > > include this with your email so we can better assist you with your > difficulties. > > thanks, > brian > > On Fri, 14 Jan 2005, Joongnam Yang wrote: > > > Hi, > > > > I did manual editting for lateral ventricles, fornix, basal ganglia, optic > > nerve, > > as illustrated in the cortical reconstruction tutorial, for both left and > > right hemispheres, and DID save them in the "wm" volume. > > Then I ran "create surface", but nothing is changed. > > > > What could have been wrong? > > > > Comments are appreciated. > > Nam. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] manual editting not implemented
use csurf only to make edits to the wm volume. then exit. and use the command line as i described to "create surfaces". that does not mean csurf is useless, but since you have many questions, this is the way i recommend you process your data until you are self-sufficient. thanks, brian On Fri, 14 Jan 2005, Joongnam Yang wrote: Thanks Brian, Does that mean csurf interface is useless for "creating surfaces" to implement the editting of major topological defects? Nam. "Brian T. Quinn" <[EMAIL PROTECTED]> 01/14/05 3:22 PM >>> hi Nam- please refrain from using the csurf interface to create surfaces. instead, run through the command line: recon-all -stage2 -subjid this will create a log file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) include this with your email so we can better assist you with your difficulties. thanks, brian On Fri, 14 Jan 2005, Joongnam Yang wrote: Hi, I did manual editting for lateral ventricles, fornix, basal ganglia, optic nerve, as illustrated in the cortical reconstruction tutorial, for both left and right hemispheres, and DID save them in the "wm" volume. Then I ran "create surface", but nothing is changed. What could have been wrong? Comments are appreciated. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
