I apologize. This is the correct info:data_type INT16dim1 280dim2 240dim3 240dim4 1datatype 4pixdim1 0.5999984741pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+

----Messaggio originale----

Da: stdp82@virgilio.it

Data: 30-mag-2013 0.30

A: sebastian.moeller1@rwth-aachen.de, "Bruce Fischl"fischl@nmr.mgh.harvard.edu

Cc: freesurfer@nmr.mgh.harvard.edu

Ogg: [Freesurfer] R: Re: very slow analysis with recon-all

Bruce and Sebastian thank you very much. I have checked the files but they are all wrong. These are the image info: data_type FLOAT32dim1 280dim2 240dim3 240dim4 1datatype 16pixdim1 0.5999984741pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_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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