Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
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,

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
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

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
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

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
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

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
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

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
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

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
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"

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread 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