Hi Wan, Looks like it had difficulty automatically finding the corpus callosum cutting plane, so you'll have to give it the coordinates manually. To do so:
Load the WM volume, and click in the dead center of the corpus callosum, in coronal view. Then switch to a sagittal plane. You should find a slice where the corp. cal. is detached from the rest of the cortical white matter. You may have to scroll around a slice or two to find that. Now, note the talairach coordinates displayed in the TkMedit tools dialog box. For example, let's say those coordinates read: 2.3 4.5 6.7 and the subject id is wan_subject. Those are the coordinates you'll manually specify when you rerun the step that separates the two hemispheres and creates their surfaces. So, run this from the command line: recon-all -stage2 -cc-xyz 2.3 4.5 6.7 -subjid wan_subject Let us know if this did not fix the problem. Note: This fix assumes that the talairach transform (wan_subject/mri/transforms/talairach.*) looks good. Good luck! On Tue, 25 Jan 2005, Wan Park wrote: > when i try to create the surface, i receive this message: > > > /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill -lval 255 > -rval 80 -ccmask -T 1 -L > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ > ponscall.dat > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/wm > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/filled > using 255 as fill val for left hemisphere. > using 80 as fill val for right hemisphere. > not using corpus callosum to mask possible location of pons. > logging cutting plane coordinates to > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ > ponscall.dat... > reading input volume...done. > searching for cutting planes...voxel to talairach voxel transform > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not > find valid seed for the cc > No such file or directory > Looking for area (min, max) = (350, 1400) > area[0] = 2435 (min = 350, max = 1400), aspect = 0.88 (min = 0.10, max > = 0.75) > need search nearby > using +/- offset search region where offset is 3..... > using +/- offset search region where offset is 6..... > using +/- offset search region where offset is 9..... > using +/- offset search region where offset is 12..... > using +/- offset search region where offset is 15..... > using +/- offset search region where offset is 18..... > using +/- offset search region where offset is 21..... > using +/- offset search region where offset is 24..... > using +/- offset search region where offset is 27..... > using +/- offset search region where offset is 30..... > using +/- offset search region where offset is 33..... > using +/- offset search region where offset is 36..... > using +/- offset search region where offset is 39..... > using +/- offset search region where offset is 42..... > using +/- offset search region where offset is 45..... > using +/- offset search region where offset is 48..... > Looking for area (min, max) = (350, 1400) > area[0] = 2001 (min = 350, max = 1400), aspect = 0.99 (min = 0.10, max > = 0.75) > need search nearby > using +/- offset search region where offset is 3..... > using +/- offset search region where offset is 6..... > using +/- offset search region where offset is 9..... > using +/- offset search region where offset is 12..... > using +/- offset search region where offset is 15..... > using +/- offset search region where offset is 18..... > using +/- offset search region where offset is 21..... > using +/- offset search region where offset is 24..... > using +/- offset search region where offset is 27..... > using +/- offset search region where offset is 30..... > using +/- offset search region where offset is 33..... > using +/- offset search region where offset is 36..... > using +/- offset search region where offset is 39..... > using +/- offset search region where offset is 42..... > using +/- offset search region where offset is 45..... > using +/- offset search region where offset is 48..... > /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not > find corpus callosum > 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... > > > could you please teach me how to solve the problem? thanks, > > wan park -- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
