Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data
I tried that and I got an error in the Mask function that excludes the
inter-hemispheric cut in matlab.
It doesn’t like the lh/rh.pial surfaces of the fsaverage.
This is the code:
0001 function mask = SurfStatMaskCut( surf );
0002
0003 %Mask that excludes the inter-hemisphere cut.
0004 %
0005 % Usage: mask = SurfStatMaskCut( surf );
0006 %
0007 % surf.coord = 3 x v matrix of surface coordinates, v=#vertices.
0008 %
0009 % mask = 1 x v vector, 1=inside, 0=outside, v=#vertices.
0010 %
0011 % It looks in -50<y<50 and -20<z<40, and mask vertices where |x|>thresh,
0012 % where thresh = 1.5 x arg max of a histogram of |x|.
0013
0014 f=(abs(surf.coord(2,:))<50 ...
0015 & abs(surf.coord(3,:)-10)<30 ...
0016 & abs(surf.coord(1,:))<3);
0017 b=(0:0.02:3);
0018 h=hist(abs(surf.coord(1,f)),b);
0019 t=b(find(h==max(h)))*1.5;
0020 mask=~(abs(surf.coord(1,:)) wrote:
You can map it onto fsaverage, which is made only from 40 subjects, so
there is a little more folding
On 01/09/2018 06:27 PM, Duran, Tugce wrote:
> Total N is 159. I have min # of 52 subjects for certain analyses. I used
avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and
thickness data.
> Can the visualization issue be fixed?
>
> Thanks!
> Tugce
>
> dur...@iupui.edu
>
> On 1/9/18, 6:19 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:
>
> This is not entirely unexpected as the volume-based average of pial
> surfaces will lose folds as you add subjects. How many subjects do
you
> have? Note that this is only a visualization issue if all your
> underlying analysis is done on the surface.
>
>
> On 01/08/2018 01:14 PM, Duran, Tugce wrote:
> >
> > Hi FS experts,
> >
> > I’m running SurfStat on my freesurfer skullstriped data (recon-all
> > with –noskullstrip flag) and getting pecan shaped brain images as
> > shown in the attached file.
> >
> > Do you know what freesurfer process (make_average_subject or glm or
> > other) is causing this issue?
> >
> > Thanks!
> >
> > *Tugce Duran, B.S.*
> >
> > /Research Technologist II/
> >
> > cid:image001.png@01D3861A.789F16C0
> > <https://medicine.iu.edu/departments/neurology/research/>
> >
> > Indiana Alzheimer Disease Center (iADC)
> >
> > Office: 317-278-7015
> >
> > dur...@iupui.edu <mailto: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
Phon
Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data
Total N is 159. I have min # of 52 subjects for certain analyses. I used avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and thickness data. Can the visualization issue be fixed? Thanks! Tugce dur...@iupui.edu On 1/9/18, 6:19 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: This is not entirely unexpected as the volume-based average of pial surfaces will lose folds as you add subjects. How many subjects do you have? Note that this is only a visualization issue if all your underlying analysis is done on the surface. On 01/08/2018 01:14 PM, Duran, Tugce wrote: > > Hi FS experts, > > I’m running SurfStat on my freesurfer skullstriped data (recon-all > with –noskullstrip flag) and getting pecan shaped brain images as > shown in the attached file. > > Do you know what freesurfer process (make_average_subject or glm or > other) is causing this issue? > > Thanks! > > *Tugce Duran, B.S.* > > /Research Technologist II/ > > cid:image001.png@01D3861A.789F16C0 > <https://medicine.iu.edu/departments/neurology/research/> > > Indiana Alzheimer Disease Center (iADC) > > Office: 317-278-7015 > > dur...@iupui.edu <mailto: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
[Freesurfer] ?h.pial_avg in make_average_subject in FS6.0
Dear Doug Greve, Where can I find the rh/lh.pial_avg file in fsaverage/surf/ created in freesurfer 6.0? Is this file named differently in FS 6.0 or do I need to process this step (where it makes rh or lh.pial_avg) separetely? Thanks, Tugce Duran ___ 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] error in mri_surf2surf FS60
Dear FS Experts, I recently got the attached error in mris_preproc and mri_surf2surf in FS 6.0. These commands work in FS 5.3. But somehow FS 60 doesn’t run the files correctly. Any ideas? Thanks, Tugce Duran lh.thickness.mris_preproc.log Description: lh.thickness.mris_preproc.log ___ 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] error in make_average_subject
Dear FreeSurfer Experts, I’m getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 128.0; 0.0 0.0 0.0 1.0; mghRead(mri/norm.mgz, -1): could not open file - Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited with ERRORS at Wed Nov 15 19:14:17 EST 2017 It appears that during the process it doesn’t create the norm.mgz file to read or open it in the later processes (I think?). What can I do to fix this error? Thanks, Tugce recon-all[1].log Description: recon-all[1].log ___ 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] make_average_subject error
Please see the attached log file. Thanks, Tugce On 11/16/17, 11:35 AM, "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: can you send the entire log file? On 11/16/2017 11:32 AM, Duran, Tugce wrote: > > Dear FreeSurfer Experts, > > I’m recently getting an error in make_average_subject and can’t find > the reason. > > Please see the following for the error log from recon-all.log: > > *Loading aseg from > /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz* > > *ASeg Vox2RAS: ---* > > *-1.0 0.0 0.0 128.0;* > > *0.0 0.0 1.0 -128.0;* > > *0.0 -1.0 0.0 128.0;* > > *0.0 0.0 0.0 1.0;* > > *mghRead(mri/norm.mgz, -1): could not open file* > > *-* > > ** > > *Labeling Slice* > > *relabeling unlikely voxels in interior of white matter* > > *mri/norm.mgz: could not load norm volume from (null)* > > ** > > *Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep > 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux* > > ** > > *recon-all -s > fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop > exited with ERRORS at Wed Nov 15 19:14:17 EST 2017* > > ** > > ** > > It appears that during the process it doesn’t create the norm.mgz file > to read or open it in the later processes (I think?). What can I do to > fix this error? > > Thanks, > > Tugce** > > > > ___ > 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. recon-all.log Description: recon-all.log ___ 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] make_average_subject error
Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 128.0; 0.0 0.0 0.0 1.0; mghRead(mri/norm.mgz, -1): could not open file - Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited with ERRORS at Wed Nov 15 19:14:17 EST 2017 It appears that during the process it doesn’t create the norm.mgz file to read or open it in the later processes (I think?). What can I do to fix this error? Thanks, Tugce ___ 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
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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@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
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:39 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:
>
> 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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf 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"
<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 *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/$PREFIX.$in
Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0
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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf 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" <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 *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
Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0
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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf 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" <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 *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
Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0
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 *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
[Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0
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 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.
