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 nicks@nmr.mgh.harvard.edu 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
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 nicks@nmr.mgh.harvard.edu 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@nmr.mgh.harvard.edu
-
Joongnam Yang -
Nick Schmansky