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...
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------------------ pass 1 (num=2853) ------------------
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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