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.Ihavealrea...
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
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.Ihavealrea...
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
durant@iupui.edu
On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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.Ihavealrea... > > 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 > > > > _______________________________________________ > 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 greve@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.
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
durant@iupui.edu
On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > durant@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 greve@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
Is there a flag like –noskullstrip where we can skip brain-stem parcellation/labeling?
Tugce
On 10/17/17, 12:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > durant@iupui.edu > > On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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.Ihavealrea... > > > > 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 > > > > > > > > _______________________________________________ > > 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 > greve@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 greve@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
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-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > durant@iupui.edu > > On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > > durant@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 > greve@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 greve@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
Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because I also did that and saw some cerebral cortex labeled as brain stem. There is no brain-stem in my skull-stripped data.
Tugce
durant@iupui.edu
On 10/17/17, 12:39 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
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-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > > > > durant@iupui.edu > > > > On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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.Ihavealrea... > > > > > > 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 > > > > > > > > > > > > _______________________________________________ > > > 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 > > greve@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 > greve@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 greve@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/
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Copy it before you run recon-all and copy it to brainmask.mgz (not to auto). If there is no brainstem, then I think it will fail
On 10/17/2017 12:55 PM, Duran, Tugce wrote:
Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because I also did that and saw some cerebral cortex labeled as brain stem. There is no brain-stem in my skull-stripped data.
Tugce
durant@iupui.edu
On 10/17/17, 12:39 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
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-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > > > > durant@iupui.edu > > > > On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > > > > durant@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 > > greve@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 > greve@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 greve@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
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I think that is the issue. Freesurfer thinks there is brainstem in the skull-stripped image. That’s why it labels whatever gray matter it sees as brain stem. We’ll add the brain stem to the data and run it like that.
Thanks! Tugce
On 10/17/17, 1:28 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Copy it before you run recon-all and copy it to brainmask.mgz (not to auto). If there is no brainstem, then I think it will fail
On 10/17/2017 12:55 PM, Duran, Tugce wrote: > Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because I also did that and saw some cerebral cortex labeled as brain stem. There is no brain-stem in my skull-stripped data. > > Tugce > > > durant@iupui.edu > > On 10/17/17, 12:39 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: > > 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-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > > > > > > > > durant@iupui.edu > > > > > > On 10/17/17, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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.Ihavealrea... > > > > > > > > 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 > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > greve@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 > > greve@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 > greve@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 greve@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/
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freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Duran, Tugce