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, std...@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.moell...@rwth-aachen.de
Data: 26-mag-2013 21.31
A: "Bruce Fischl"<fis...@nmr.mgh.harvard.edu>
Cc: <std...@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, std...@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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