how long have you waited? On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
Hi, Freesurfers I am getting some interesting hippocampal surfaces with the following steps: 1- recon-all -all -hippo-subfields 2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes) 3- a custom OCTAVE script to segment the concatenated volume from step 2 into Head, Body and Tail 4- mri_binarize Head, Body and Tail volumes from step 3 5- mri_tessellate the binary masks from step 4 6- mri_smooth the surfaces from step 5 Using freeview I got a screenshot showing both hippocampi segmented (hipposurf3d.png is attached). This approach worked well for 16 subjects up to step 5. Step 6 was completed as well in 13 out 16 subjects. The only problem was during left hippocampal body smoothing in 3 subjects (all the other surfaces from all 16 subjects in were smoothed with no problem). For these 3 surfaces, mris_smooth simply freezes, with no error message. I must press control + C to quit the program. During the freezing I noticed high CPU use. It follows the exactly command I used and the screen output. mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody using Gaussian curvature smoothing with norm 5.00 with 2 smooth steps averaging curvature for 1 iterations smoothing for 1 iterations smoothing surface tessellation for 1 iterations... ------------------------------------------------------ ------------------------------------------------------ ------------------ pass 1 (num=2853) ------------------ ------------------------------------------------------ ------------------------------------------------------ If I supress the gaussian parameters and run just something like: mris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody or even mris_smooth -nw surfLeftHippoBody lh.surfHippoBody I got the smoothed surface with no errors but the final quality is not as good as when I use the gaussian parameters. I am attaching one of the problematic surface files so you can check it (surfLeftHippobody). Intersting if I use a surface with all left hippocampus (including head, problematic body and tail and) smoothing completes without error Thank you very much for any help. Marcos
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