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, "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:
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 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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> > > >
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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
> > >
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> > >
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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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> >
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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
> Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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