Re: Re: [Freesurfer] error in 'create surface'
Nam, The newer versions of freesurfer (those within the past year) contain the major libraries and toolkits upon which freesurfer depends (Tcl/Tk/Tix/BLT, GSL, MNI, FSL), so it should be straightforward to install a new version. See: http://surfer.nmr.mgh.harvard.edu/fswiki/Download Basicaly, just get the tarball, untar anywhere (for example, to /usr/local), and put this in your .cshrc file: setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Nick On Thu, 2006-06-01 at 17:27 -0400, Joongnam Yang wrote: > Thanks, Nick, > > If I install a new version of FS, would it be too much of hassle? > > Because I am in the middle of data analysis for a project using the > old version, and I remember I had a big trouble installing different > libraries for Freesurfer for the old version, which was a daunting job. > > Nam. > > >>> Nick Schmansky <[EMAIL PROTECTED]> 06/06/01 오후 2:54 >>> > Nam, > > The csurf application is no longer supported (and has been removed from > the newest release). The recon-all script now performs all processing > stages, where the three main stages are -autorecon1, -autorecon2 and - > autorecon3 (-stage1 is a deprecated option). > > You may want to see our new tutorial, here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial > > to learn what sorts of problems can occur during the various stages. > > It's hard to say from your email what the problem may be, but it could > be a bad Talairach alignment. The tutorial discusses this. Note: you > should not see the brain stem after the image has been skull-stripped > (which occurs during the -autorecon1 stage). > > Nick > > > On Thu, 2006-06-01 at 14:40 -0400, Joongnam Yang wrote: > > Hi all, > > > > I posted a question, but for some reason, I didn't get any response. > > Please help me on this. > > Here is the question. > > > > I ran 'process volume' and 'create surface' on csurf. > > The created surface (left inflated) has brain stem attached to it. > > So, I editted 'wm' slices to get rid of it, and ran 'create surface' > again. > > No change took place. > > I tried commandline 'recon-all -stage1 -subjid ID', with no luck. > > > > Would someone suggest any comment on this? > > > > 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: Re: [Freesurfer] error in 'create surface'
Thanks, Nick, If I install a new version of FS, would it be too much of hassle? Because I am in the middle of data analysis for a project using the old version, and I remember I had a big trouble installing different libraries for Freesurfer for the old version, which was a daunting job. Nam. >>> Nick Schmansky <[EMAIL PROTECTED]> 06/06/01 오후 2:54 >>> Nam, The csurf application is no longer supported (and has been removed from the newest release). The recon-all script now performs all processing stages, where the three main stages are -autorecon1, -autorecon2 and - autorecon3 (-stage1 is a deprecated option). You may want to see our new tutorial, here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial to learn what sorts of problems can occur during the various stages. It's hard to say from your email what the problem may be, but it could be a bad Talairach alignment. The tutorial discusses this. Note: you should not see the brain stem after the image has been skull-stripped (which occurs during the -autorecon1 stage). Nick On Thu, 2006-06-01 at 14:40 -0400, Joongnam Yang wrote: > Hi all, > > I posted a question, but for some reason, I didn't get any response. > Please help me on this. > Here is the question. > > I ran 'process volume' and 'create surface' on csurf. > The created surface (left inflated) has brain stem attached to it. > So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. > No change took place. > I tried commandline 'recon-all -stage1 -subjid ID', with no luck. > > Would someone suggest any comment on this? > > 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] error in 'create surface'
Nam, The csurf application is no longer supported (and has been removed from the newest release). The recon-all script now performs all processing stages, where the three main stages are -autorecon1, -autorecon2 and - autorecon3 (-stage1 is a deprecated option). You may want to see our new tutorial, here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial to learn what sorts of problems can occur during the various stages. It's hard to say from your email what the problem may be, but it could be a bad Talairach alignment. The tutorial discusses this. Note: you should not see the brain stem after the image has been skull-stripped (which occurs during the -autorecon1 stage). Nick On Thu, 2006-06-01 at 14:40 -0400, Joongnam Yang wrote: > Hi all, > > I posted a question, but for some reason, I didn't get any response. > Please help me on this. > Here is the question. > > I ran 'process volume' and 'create surface' on csurf. > The created surface (left inflated) has brain stem attached to it. > So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. > No change took place. > I tried commandline 'recon-all -stage1 -subjid ID', with no luck. > > Would someone suggest any comment on this? > > 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
