Hi Jane, hi Bruce,

On Jun 18, 2013, at 18:17 , Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Jane

that means it is trying to correct the topology of a very large defect. 46K vertices is about 1/3 of a normal human hemisphere. Check the ?h.orig.nofix and see if something big has gone wrong - the skull being attached or the cerebellum or something like that. I don't have much experience with NHP data, so hopefully someone else on the list can chime in.

For NHPs I would recommend to have a look at the filled.mgz. After selecting pons and corpus callosum cutting planes I would recommend: mri_fill -a ../scripts/tmp_ponscc.cut.log -Cv corpuscallosum_coordinates -Pv pons_coordinates ${src_dir}/wm.mgz ${targ_dir}/filled.mgz tkmedit -f ${src_dir}/filled.mgz (please set src_dir accordingly). If the filled.mgz attributes the cerebellum to any one hemisphere (as shown in two shades of gray) do not bother to run recon-all to get the surface reconstructed, it will take forever and the results are not useable. This step should finish well below 8 hours.

best Sebastian

cheers Bruce

On Tue, 18 Jun 2013, Jane Qu wrote:

...

Hi freesurfers! I am new to freesurfer and have encountered a problem with surface generation. I am working with a non-human primate anatomical volume. I finished segmenting the white matter and am on this next step. I think, however, that the step where the surface is generated from wm.mgz is crashing (I started the process last night and it has not finished and does not appear to be moving forward). Does anybody know why this might be happening? How long should I expect this step to take? I have attached below some of the messages I'm receiving. Thanks in advance! Jane

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