I think that is the issue. Freesurfer thinks there is brainstem in the
skull-stripped image. That’s why it labels whatever gray matter it sees as
brain stem.
We’ll add the brain stem to the data and run it like that.
Thanks!
Tugce
On 10/17/17, 1:28 PM,
Copy it before you run recon-all and copy it to brainmask.mgz (not to
auto). If there is no brainstem, then I think it will fail
On 10/17/2017 12:55 PM, Duran, Tugce wrote:
> Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to
> brainmask.auto.mgz and a link from
Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to
brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because
I also did that and saw some cerebral cortex labeled as brain stem. There is no
brain-stem in my skull-stripped data.
Tugce
dur...@iupui.edu
On
No, but I think if you copy it to brainmask.mgz that it will then use that
On 10/17/2017 12:28 PM, Duran, Tugce wrote:
> Is there a flag like –noskullstrip where we can skip brain-stem
> parcellation/labeling?
>
> Tugce
>
> On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
Is there a flag like –noskullstrip where we can skip brain-stem
parcellation/labeling?
Tugce
On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" wrote:
if they look
if they look ok, then I think they are ok
On 10/17/2017 12:05 PM, Duran, Tugce wrote:
> That is exaclty right! But how did freesurfer respond to that, performing the
> skull stripping to skull-stripped data?
> Should I trust the results since they looked okay?
>
> Tugce
>
>
> dur...@iupui.edu
That is exaclty right! But how did freesurfer respond to that, performing the
skull stripping to skull-stripped data?
Should I trust the results since they looked okay?
Tugce
dur...@iupui.edu
On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve"
if you put -all AFTER the -noskullstrip, then it would have performed
the skull stripping
On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Team,
>
> I have recently submitted my skull-stripped data into FreeSurfer v6.
> Since this is a separate process than the default recon-all