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

durant@iupui.edu