OK. So do you have any other suggestions? Is there some minor difference between my version and yours that would explain this behavior. Other settings to try?
Darren
On Wed, Sep 5, 2012 at 4:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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 <fischl@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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