Hi Jonathan,
if you load the filled.mgz you should be able to see whether the cerebellum is
still attached, if so you might want to either edit the wm.mgz, the brainmask,
or make sure pons and cc were properly detected. For my non-human subjects I
have to always check the filled.mgz before running the actual surface
reconstruction otherwise every single one of them will try to reconstruct the
cerebellum, while taking an eternity.
best
sebastian
On Jul 19, 2011, at 12:56 , Bruce Fischl wrote:
> Hi Jonathan
>
> usually that means there is a giant defect that will not be corrected
> properly (e.g. cerebellum or skull attached). Did you check the
> ?h.inflated.nofix or ?h.orig.nofix surfaces?
>
> cheers
> Bruce
>
>
> On Tue, 19 Jul 2011, Jonathan McDaniel wrote:
>
>> Hi,
>> I have been running a surface reconstruction for over 19 days now, and it is
>> still in the process of correcting defects. Based on how long
>> it took to do one hemisphere (it is now on the second) it appears it will be
>> done hopefully within 3 days. I have been concurrently
>> running other subjects on the same quadcore machine, using 3 of the 4
>> processors to perform the recons, and they have been finishing in a
>> normal amount of time. Has anyone else had a brain take this long to run?
>> Should I suspect that something is wrong with the inputted
>> dicom files? Are manual edits necessary to fix some of the defects to speed
>> up the process?
>> Thanks for your answers!
>> Jonathan
>>
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