[Freesurfer] Missing MNI coordinates
Hi I just discovered that I'm lacking the MNI coordinates in Freesurfer2004-02-18. I just updated this version with the new mri_convert and mri_watershed fix (putting these in the freesurfer/bin/Linux directory). That couldn't create this problem? Any suggestions appreciated. Thanks, Kristine ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Missing MNI coordinates
the MNI coords are only shown if the talairach.xfm exists, and if view->info->MNI coords is checked. cheers, Bruce On Thu, 21 Oct 2004, Kristine Beate Walhovd wrote: Hi I just discovered that I'm lacking the MNI coordinates in Freesurfer2004-02-18. I just updated this version with the new mri_convert and mri_watershed fix (putting these in the freesurfer/bin/Linux directory). That couldn't create this problem? Any suggestions appreciated. Thanks, Kristine ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] when I am creating the surface
I start with the filling of white matter but after a while I am receiving this massage: (...) using +/- offset search region where offset is 45. using +/- offset search region where offset is 48. /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... Command Finished could you help me with this? thanks, wan park___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] when I am creating the surface
Hi Wan, you can always manually select seed points in the left and right hemisphers and in the pons and corpus callosum, then specify them in the mri_fill command line: mri_fill -lh -rh -p -cc wm filled from the subject's mri directory. The better way to do this thought is to use the MNI auto talairaching and the fill will work much better. cheers, Bruce On Thu, 21 Oct 2004, Wan Park wrote: I start with the filling of white matter but after a while I am receiving this massage: (...) using +/- offset search region where offset is 45. using +/- offset search region where offset is 48. /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... Command Finished could you help me with this? thanks, wan park ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
