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 > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > 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 > > > > 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/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > whom it is > > addressed. If you believe this e-mail was sent to you in error > and the e-mail > > contains patient information, please contact the Partners > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent > to you in error > > but does not contain patient information, please contact the > sender and properly > > dispose of the e-mail. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > 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 > > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
