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.
