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