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
