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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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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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--
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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