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 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
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 behalf
of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
>
> 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
> >
> > On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
> >
> > 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
–all, I
> > > followed the recommended steps that are posted on the
FSwiki website,
> > > here is the link for it:
> > >
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
> > >
> > > By doing so, I accidentally submitted my data both with
*recon-all
> > > -autorecon1 -noskullstrip -s <subjid> *and *–all *flag at
the beginning.
> > >
> > > Using PBS script, here is an example of this:
> > >
> > > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1
E008_V1 E010_V1
> > > E011_V1 E013_V1 E014_V1 E015_V1"
> > >
> > > echo $list
> > >
> > > OUTDIR="/pathtodirectory/logs_KT"
> > >
> > > PREFIX="recon-all"
> > >
> > > for index in $list; do
> > >
> > > recon-all *–autorecon1 –noskullstrip*-i
> > > /pathtodirectory/$index/"$index".nii -subject $index -sd
> > > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
> > > 2>$OUTDIR/$PREFIX.$index.err &
> > >
> > > done
> > >
> > > wait
> > >
> > > I forgot to remove the flag –all at the end of this command.
> > > Therefore, freesurfer v6 processed my data all the way till
the end
> > > and Viola it worked! And I am wondering If I could trust
this data
> > > since it looks OKAY when I look at the segmentation,
parcellation. Can
> > > I trust this skull-stripped processes data with –autorecon1
> > > –noskullstrip and –all options?
> > >
> > > I hope my explanation and question makes sense.
> > >
> > > Thanks,
> > >
> > > Tugce Duran
> > >
> > > dur...@iupui.edu
> > >
> > >
> > >
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
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> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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