I don't understand. Did you look at the defects in tksurfer? Or the aseg? You need to go through the processing steps and identify what failed Bruce On Thu, 30 May 2013, stdp82@virgilio.it wrote:
Bruce and Sebastian thank you very much. I have checked the files but they are all wrong.
These are the image info:
data_type FLOAT32 dim1 280 dim2 240 dim3 240 dim4 1 datatype 16 pixdim1 0.5999984741 pixdim2 1.0416666269 pixdim3 1.0416666269 pixdim4 0.0000000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
Waiting for your feedback.
Thank you very much.
Stefano
----Messaggio originale---- Da: sebastian.moeller1@rwth-aachen.de Data: 26-mag-2013 21.31 A: "Bruce Fischl"fischl@nmr.mgh.harvard.edu Cc: stdp82@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] very slow analysis with recon-all
Hi Stefano, hi Bruce,
sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT part of either hemisphere. (In my cases typically I then have to either edit the wm.mgz, the brain mask, or the pons cutting plane, but I guess that is NHP specific). Now wouldn't that filled.mgz check not also work for human recons?
best Sebastian
On May 26, 2013, at 21:13 , Bruce Fischl wrote:
Hi Stefano
a defect with over 60K vertices is more than 1/2 the size of a typical
hemisphere, so something has gone badly wrong. Have you checked the skull stripping? The aseg? The talairach? There shouldn't be a defect that big - you will need to figure out why
cheers Bruce On Sun, 26 May 2013, stdp82@virgilio.it wrote:
Hi list, I'm running recon-all on two T1 but the command is for two days on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). Is it ok? What's happen? Thanks, Stefano
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