Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce 
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-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  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
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Douglas N Greve"  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-boun...@nmr.mgh.harvard.edu on 
behalf of Douglas N Greve"  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" 
 
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  *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
>  >  >  >

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve 
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
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Douglas N Greve"  gr...@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-boun...@nmr.mgh.harvard.edu on 
> behalf of Douglas N Greve"  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"  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  *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.

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce 
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


dur...@iupui.edu

On 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  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-boun...@nmr.mgh.harvard.edu on behalf 
of Douglas N Greve"  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"  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  *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/
>

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve 
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"  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"  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  *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.
>  >
>  >
>  >
>  >

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce 
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"  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"  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  *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/
>  
>  ___
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>  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.
>  
>
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-- 
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

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve 
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"  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  *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/

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Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce 
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"  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  *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/

___
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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.



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Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve 
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  *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/

___
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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.