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
Phone Number: 617-724-2358
Fax: 617-726-7422
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