Hi Peggy, Your control points file might not be saving. Make sure there is a tmp directory in the directory for each subject. Inside this directory should be a file called control.dat. If that file isn't there, you need to modify the COR-.info file in the $SUBJECTS_DIR/$SUBJECT/mri/T1 directory. Change "ras_good_flag 1" to "ras_good_flag 0" before opening tkmedit. Save the COR-.info file, then open tkmedit for that subject. Save your control points again, and the control.dat file should show up in your $SUBJECTS_DIR/$SUBJECT/tmp directory.

Good luck, Jon

On 6/9/05 1:46 PM, "peggy christidis" christip@mail.nih.gov wrote:

Hey everyone,

Someone has given me a monkey volume (it's actually the average of 4 volumes and the gray-white matter contrast is pretty good) and I need to make a surface from it. I've never dealt with non-human datasets, but I did read in the freesurfer mailing archives that control points must always be added to a monkey T1 volume in order to get a decent wm segmentation. I ran recon-all stage1 and I got a first pass surface, and indeed I need to add control points because there is alot of white matter in the frontal lobes that is not being included in the segmentation. So I selected some control points (in the T1 volume, within the white matter), and then I ran this command: recon-all stage1 -usecontrolpoints -subjid monkey_surf

I looked at the output and it doesn't seem to have helped at all. The segmentation still doesn't include the wm where the control points were added. What am I doing wrong? I've attached a jpg file to illustrate my problem.

Thanks, Peggy _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer