our internal development version.
On Wed, 5 Sep 2012, Darren Gitelman
wrote:
Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
Is that the same as the one you are using or are you referring to an
internal development version?
I will try Nick's suggestion as well.
Darren
On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
I'm running it now with the current dev version and it's passed
the skull
stripping stage and it seems to have worked fine...
On Wed,
5 Sep 2012, Nick Schmansky wrote:
> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwise the prior
brainmask.mgz will be
> retained and the new one will be saved as brainmask.auto.mgz.
>
> Nick
>
>
> On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
>> Nick, List:
>>
>>
>>
>> Still no luck with this data. See attached as an example.
>>
>>
>>
>> To get to this point I had run:
>>
>>
>>
>> recon-all -all
>>
>>
>>
>> This ran to the error: mri_watershed Error: GLOBAL region of the
>> brain empty !
>>
>>
>>
>> Then I followed your recommendation below
>>
>>
>>
>> recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no
errors
>> and then
>>
>> recon-all -s <subjid> -autorecon2 -autorecon3
>>
>>
>>
>> This produced the result attached.
>>
>>
>>
>> I then deleted this directory and re-imported all the dicom data
for
>> this subject. Looked at the images, which look fine.
>>
>> Then I ran recon-all -s <subjid> -autorecon1
>>
>>
>>
>> This fails with the mri_watershed error.
>>
>>
>>
>> Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
>>
>>
>>
>> This runs without error but when I look at the brainmask.mgz it
looks
>> just like the attached image.
>>
>>
>>
>> Is there some way to set the thresholds differently? The T1 image
>> looks fine to me although perhaps the intensity is slightly less
than
>> usual, but it doesn't seem particularly noisy.
>>
>>
>>
>> Darren
>>
>>
>>
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>
>
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