Re: [Freesurfer] repost aseg.mgz error

[Jasmin Alves]

Hi Douglas,

Thanks for the reply, this was my thought too. The files have been uploaded.

Thanks!
Jasmin

On Fri, Aug 12, 2016 at 12:59 PM, Douglas N Greve  wrote:

> I'm guessing that the registration failed on it. Can you tar up the
> subject and upload to our file drop (URL) below?
>
> On 08/12/2016 12:00 PM, Jasmin Alves wrote:
> > Dear Freesurfer
> >
> > I encountered an error on the aseg mask for a participant, both
> > hemispheres for the aseg appear on one hemisphere of the brain mask.
> >
> > I ran it a few times and I also used different T1s but it consistently
> > showed this error.
> >
> > Is there a way I can correct this?
> >
> > Thanks,
> > Jasmin
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> > ___
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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
>
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-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] FW: TRACULA re-init error

[Anastasia Yendiki]

Hi - Does this directory exist?

ERROR: fio_pushd: 
/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni

I'd have to see the entire trac-all.log file to tell you for sure. The 
first error may show up earlier than the one that causes the crash.

Thanks,

a.y

On Mon, 8 Aug 2016, Song, Daniel wrote:

> 
> 
> Dan
> 
> _
> From: Ostrowski, Lauren
> Sent: Monday, August 08, 2016 4:08 PM
> To: Song, Daniel
> Subject: FW: TRACULA re-init error
> 
> 
> _
> From: Ostrowski, Lauren
> Sent: Monday, August 08, 2016 4:04 PM
> To: Freesurfer@nmr.mgh.harvard.edu
> Subject: TRACULA re-init error
> 
> Hi all,
> 
> I'm running into a problem with TRACULA, when I try to re-initialize tracts 
> that failed to reconstruct during the first
> run. I have set reinit = 1 in the configuration file and specified the 
> particular tracts that I want to reconstruct, but
> when I try to run the "trac-all -prior" step, I keep getting this error 
> message:
> 
> INFO: SUBJECTS_DIR is /autofs/cluster/neuromind/cat/bects/subjects
> INFO: Diffusion root is /cluster/neuromind/cat/bects/subjects/pBECTS001/trac
> Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev
> trac-preproc -c 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/dmrirc.local
>  -log /cluster/neuromi
> nd/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.log -cmd 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/
> trac/pBECTS001/scripts/trac-all.cmd
> #-
> /usr/local/freesurfer/dev/bin/trac-preproc 
> #-
> #@# Priors Mon Aug  8 15:53:46 EDT 2016
> /usr/local/freesurfer/dev/bin/dmri_train --outdir 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/m
> ni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt 
> --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/
> mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois 
> dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/m
> ni/fmajor_PP_roi2.bbr.nii.gz --bmask 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain
> _mask.bbr.nii.gz --fa 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz
>  --cptdir /clus
> ter/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg 
> /cluster/neuromind/cat/bects/subjects/pBECTS0
> 01/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc
> ERROR: fio_pushd: 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni
> cwd /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/dlabel/mni
> cmdline /usr/local/freesurfer/dev/bin/dmri_train --outdir 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/
> dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist 
> /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg
>  dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 
> --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz 
> dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lo
> wb_brain_mask.bbr.nii.gz --fa 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz
>  --cptd
> ir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff 
> --reg /cluster/neuromind/cat/bects/subjects
> /pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc 
> sysname  Linux
> hostname truffles
> machine  x86_64
> user lo941
> Output directory: 
> /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni
> Output directory in test subject's space: 
> /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/di
> ff
> Output base: fmajor_PP_avg33_mni_bbr
> Training subject directory list: /tmp/subj33.pBECTS001.15581.txt
> Location of streamline files relative to base: dlabel/mni/fmajor_PP.bbr.trk
> Location of start ROI files relative to base: 
> dlabel/mni/fmajor_PP_roi1.bbr.nii.gz
> Location of end ROI files relative to base: 
> dlabel/mni/fmajor_PP_roi2.bbr.nii.gz
> Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
> Label ID's from aparc+aseg to add to cortex mask: 0
> Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
> Brain mask for output subject: Segmentation fault (core dumped) 
> Linux truffles 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 
> x86_64 x86_64 x86_64 GNU/Linux
> trac-preproc exited with ERRORS at Mon Aug  8 15:53:46 EDT 2016
> 
> Any help would be very much appreciated. It seems to me that TRACULA can't 
> find the aparc+aseg labels, but when I looked
> at 

Re: [Freesurfer] TRACULA tract endpoints on cortical surface

[Anastasia Yendiki]

Hi Barbara - This can be done with mri_vol2surf. The projection that's 
described in that passage can be done with --projdist-max -6 6 1, and the 
surface smoothing with --surf-fwhm 6. There are other options in 
mri_vol2surf, I'd recommend playing with the settings to see what works 
better for your data.

Best,

a.y


On Fri, 5 Aug 2016, Barbara Kreilkamp wrote:

>
> Dear Freesurfers and TRACULA experts,
>
> Thank you for your help so far. I am trying to map the endpoints of the
> tract probability distributions onto the cortical surface (as mentioned
> in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
>
> I've somehow gathered that I need to do this (example one endpoint):
>
> flirt -ref /mri/orig/T1.nii.gz -in
> dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init
> /dmri/xfms/diff2anat.bbr.mat
>
> I then loaded the images in Freeview and they look reasonable together
> with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv
> dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
>
> What I don't get is how to do this:
>
> "we projected the tract endpoints onto the gray/white matter surface by
> sampling along the surface normal vector, anywhere within 6 mm (3
> DWI-space voxels) of the gray/white junction and then smoothing along
> the surface with a 2D Gaussian kernel of 6mm full width at half max."
> (Solsnes et al. 2016)
>
> Any help would be greatly appreciated.
>
> Best wishes,
> Barbara
>
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Re: [Freesurfer] repost aseg.mgz error

[Douglas N Greve]

I'm guessing that the registration failed on it. Can you tar up the 
subject and upload to our file drop (URL) below?

On 08/12/2016 12:00 PM, Jasmin Alves wrote:
> Dear Freesurfer
>
> I encountered an error on the aseg mask for a participant, both 
> hemispheres for the aseg appear on one hemisphere of the brain mask.
>
> I ran it a few times and I also used different T1s but it consistently 
> showed this error.
>
> Is there a way I can correct this?
>
> Thanks,
> Jasmin
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
> ___
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-- 
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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
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Re: [Freesurfer] Recon-all

[Douglas N Greve]

Yes, but if you have edited your data in any way, FS will notice this 
and keep your edits.

On 08/12/2016 11:43 AM, Heidi Foo wrote:
> Hi Allison,
>
> Thanks for the reply. Does that mean I can't use the preprocessed 
> images from 5.3 and run it with 6.0 but I'll have to use the raw T1 
> images?
>
> Thanks.
>
> Regards,
> Heidi
>
> On Friday, 12 August 2016, Allison Moreau 
> > 
> wrote:
>
> Hi Heidi,
>
> Once 6.0 is released and you have installed it, you can simply
> source that version of FreeSurfer and rerun your subjects the same
> way you did for 5.3.
>
> Best,
> Allison
>
> On 08/12/2016 06:02 AM, Heidi Foo wrote:
>> Hi FreeSurfer Team,
>>
>> I have done recon-all using FS 5.3 and I would like to run the
>> recon-ed images from 5.3 in FS 6.0. May I know how I should go
>> about doing that?
>>
>> Thank you.
>>
>> Regards,
>> Heidi Foo
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>
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-- 
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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
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[Freesurfer] repost aseg.mgz error

[Jasmin Alves]

Dear Freesurfer

I encountered an error on the aseg mask for a participant, both hemispheres
for the aseg appear on one hemisphere of the brain mask.

I ran it a few times and I also used different T1s but it consistently
showed this error.

Is there a way I can correct this?

Thanks,
Jasmin

-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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[Freesurfer] Postdoctoral Position in pediatric imaging: Boston Children's Hospital/Harvard Medical School

[Gaab, Nadine]

Postdoctoral Position at Boston/Children's Hospital & Harvard Medical School

The GaabLab (gaablab.com) at the Laboratories of Cognitive 
Neuroscience in collaboration with the Fetal-Neonatal Neuroimaging and 
Developmental Science 
Center
 at Boston Children's Hospital invites applications for a NICHD funded 
post-doctoral associate in the area of developmental cognitive 
neuroscience/pediatric (f)MRI. Available resources include a 3.0T MRI scanner, 
a child-friendly Mock scanner and analysis platforms based in MATLAB/UNIX. The 
candidate will be expected to oversee the analysis of pediatric and infant 
(f)MRI experiments, analyze behavioral and (f)MRI data, develop new analysis 
tools, prepare manuscripts for publication, and participate in conferences.

The NICHD funded project aims to characterize trajectories of early structural, 
functional, and metabolic brain development in infants with and without a 
familial risk of developmental dyslexia, and intergenerational transmission of 
brain alterations associated with language-based learning disabilities will 
further be examined. The successful applicant should have a doctoral degree in 
a field related to developmental cognitive neuroscience (e.g., cognitive 
neuroscience, neuroscience, psychology, developmental psychology, medicine) or  
a background in electrical engineering, biomedical engineering or computer 
science. The successful applicant must possess excellent English verbal and 
written communication skills. Applicants are expected to have a very strong 
research background in the design and analysis of functional brain-imaging 
experiments. Experience with (f)MRI analyses programs (e.g., SPM, FSL, 
Freesurfer, AFNI) a must. Programming skills (MATLAB, C++; Python) are 
desirable and experience with MVPA or connectivity analyses a plus. Experience 
with the analysis of pediatric neuroimaging data sets and language and reading 
research are useful. Approximate start date is fall 2016 (the earlier the 
better). Successful applicants will be appointed at Children's Hospital Boston 
and Harvard Medical School. For consideration please send a statement of 
interest, a CV and a list of three potential referees via email to Nadine Gaab, 
PhD 
(nadine.g...@childrens.harvard.edu). 
The search will continue until the position is filled.


"If we knew what it was we were doing, it would not be called research, would 
it?" A. Einstein (1879-1955)

Nadine Gaab, PhD
Associate Professor of Pediatrics
Boston Children's Hospital/Harvard Medical School
Department of Medicine/Division of Developmental Medicine
Laboratories of Cognitive Neuroscience
Mail stop code: BCH3178
1 Autumn Street (Office 643); Boston, MA 02115
nadine.g...@childrens.harvard.edu
phone: 857-218-3021
www.gaablab.com

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Re: [Freesurfer] Recon-all

[Heidi Foo]

Hi Allison,

Thanks for the reply. Does that mean I can't use the preprocessed images
from 5.3 and run it with 6.0 but I'll have to use the raw T1 images?

Thanks.

Regards,
Heidi

On Friday, 12 August 2016, Allison Moreau 
wrote:

> Hi Heidi,
>
> Once 6.0 is released and you have installed it, you can simply source that
> version of FreeSurfer and rerun your subjects the same way you did for 5.3.
>
> Best,
> Allison
>
> On 08/12/2016 06:02 AM, Heidi Foo wrote:
>
> Hi FreeSurfer Team,
>
> I have done recon-all using FS 5.3 and I would like to run the recon-ed
> images from 5.3 in FS 6.0. May I know how I should go about doing that?
>
> Thank you.
>
> Regards,
> Heidi Foo
>
>
> ___
> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] REPOST: problem with Qdecrc file

[Martin Reuter]

Hi Clara,
Try to start qdec in the same directory. If that fails create a qdec sub directory underneath the subjects _dir and put the files there.
Best Martin
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[Freesurfer] REPOST: problem with Qdecrc file

[Clara Kühn]

Dear FreeSurfer experts,

I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating 
the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab 
when I want to chose a measure.

the file is in the same directory the table.dat file is in. What might be the 
problem?

Thank you for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
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E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] Recon-all

[Allison Moreau]

Hi Heidi,

Once 6.0 is released and you have installed it, you can simply source 
that version of FreeSurfer and rerun your subjects the same way you did 
for 5.3.


Best,
Allison

On 08/12/2016 06:02 AM, Heidi Foo wrote:

Hi FreeSurfer Team,

I have done recon-all using FS 5.3 and I would like to run the 
recon-ed images from 5.3 in FS 6.0. May I know how I should go about 
doing that?


Thank you.

Regards,
Heidi Foo


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[Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear experts,

I am in trouble with two ways of computing mean intensity with mri_segstats.

First I have used on .annot files with three different labels inside (SegId
1 to 3) :

*mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*

which give me those results:
# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range
  1   1 2780514182.6  cluster-0018.8194
1.4351 6.210514.2947 8.0842
  2   2  2321 1047.3  cluster-002   10.3661
1.0848 8.837512.9317 4.0942
  3   3   552  313.1  cluster3  10.3365
0.4711 9.371911.8694 2.4975

Second I have created on .label files containing the three segmented labels
(SegId 1 to 3) and used this label with mri_segstats:

*mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i
lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum *

which give me those results:
*# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
Max Range  *
*  1   1 3067815542.9  Seg0001 8.9637 1.4701 6.2105
 14.2947 8.0842 *

I verified if I obtained the same results with the two ways (.annot or
.label) and everything is fine comparing NVertices, Area_mm2 but Mean in
first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label
file Mean = 8.9637.

Did I have miss anything and how is computed mean intensity ?

Many thanks in advance.

Best regards,
Matthieu
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[Freesurfer] Recon-all

[Heidi Foo]

Hi FreeSurfer Team,

I have done recon-all using FS 5.3 and I would like to run the recon-ed
images from 5.3 in FS 6.0. May I know how I should go about doing that?

Thank you.

Regards,
Heidi Foo
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Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 14

[Caroline Beelen]

The error is: 
"Mapping unhit to unknown.  Found 137851 unhit vertices". The file is made, but 
when trying to select it from the annotation tab in Freeview, Freeview crashes 
too.

Regards, Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens 
freesurfer-requ...@nmr.mgh.harvard.edu
Verzonden: donderdag 11 augustus 2016 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 150, Issue 14

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. aseg.stats data output (shi yao wang)
   2. mri_glmfit-sim problem (miracle ozzoude)
   3. Re: mri_glmfit-sim problem (miracle ozzoude)
   4. Re: Registration of low-resolution EPI time series to CVS MNI
  (avoiding resampling) (Douglas N Greve)
   5. Re: resample structural ROI in functional space? (Douglas N Greve)
   6. Re: query about the "normal range" in aseg.stats (Douglas N Greve)
   7. Re: aseg.stats data output (Douglas N Greve)
   8. Re: Problems with QDEC (Douglas N Greve)
   9. Re: group analysis/ region of interest (ROI) approach
  (Douglas N Greve)
  10. Re: Inquiries about QDEC inflated surface (Douglas N Greve)
  11. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve)
  12. Re: Fw: Running recon-all with T1 and FLAIR (Douglas N Greve)
  13. Re: myaparc (Douglas N Greve)
  14. Re: Qdec Generate Stats Data Table Error (Douglas N Greve)
  15. Re: bbregister problem in FS5.1 (Douglas N Greve)
  16. Re: Error with qdec (Douglas N Greve)
  17. Re: Assessing local correlations across 2 modalities
  (Douglas N Greve)
  18. Re: FS V6.0 GTM PVC ROI definition (Pradeep)
  19. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve)
  20. Re: Retinotopy questions (Douglas N Greve)
  21. how to run correlation analysis between cortical thickness
  and cognitive function (Liu Y)
  22. Re: how to run correlation analysis between cortical
  thickness and cognitive function (Douglas N Greve)


--

Message: 1
Date: Wed, 10 Aug 2016 12:38:45 -0400
From: shi yao wang 
Subject: [Freesurfer] aseg.stats data output
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

Dear FS experts:
How can I only out put the volume value in the aseg.stats file?

I applied following command:  but it will produce a table with lots of
values such as brainsegvol, brainsegvolnotvent, which I donot want to use.

thanks

asegstats2table --subjects 004 021 040 067 080 092 \
  --segno 11 17 18 \
  --tablefile aseg.vol.table
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--

Message: 2
Date: Wed, 10 Aug 2016 12:50:47 -0400
From: miracle ozzoude 
Subject: [Freesurfer] mri_glmfit-sim problem
To: Douglas N Greve 
Message-ID:

Re: [Freesurfer] qdec error

[Haakon Ramsland Hol]

 Hi Kaja.
This is not an answer from the official group, but I am used to linux so i ve 
seen this error before. 
This particular error is printed out when the GL installation doesn't include 
the GLX extensions in an X window environment (GLX not found. Aborting.). Check 
to see if there are any GLX packages available on this platform that are 
missing.

Kind regards
Haakon Ramsland Hol


Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] p vegne av Jasinska, Kaja 
[kaja.jasin...@yale.edu]
Sendt: 12. august 2016 00:30
Kopi: freesurfer@nmr.mgh.harvard.edu
Emne: Re: [Freesurfer] qdec error
Hi. My first answer in this list. So
Hello,
When I'm loading qdec, I get the following error messages. Can you please help. 
Thanks.
Kaja


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 612

vtkXOpenGLRenderWindow (0x7084e40): GLX not found.  Aborting.

--
---
Kaja K. Jasinska, Ph.D.
Post-Doctoral Research Associate
Haskins Laboratories
300 George Street Suite 900
New Haven, CT 06511
USA: 203-865-6163 ext 315
Cote d’Ivoire: (+225) 77 62 42 28
Skype: kaja.jasinska
kaja.jasin...@yale.edu
www.haskins.yale.edu/staff/jasinska/
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[Freesurfer] Inter-rater and intra-rater reliability

[Annemarie Brandhofe]

Dear FreeSurfer experts,



I have a question regarding manual interventions during the recon-all
script of FreeSurfer 5.3.0 (i.e. setting control points, performing white
matter edits). How can we check for inter- and intra-rater reliability?

In an earlier post you mentioned an intra- and inter-rater reliability
study you did. Could you tell me the name of this publication?



Thank you in advance for your help!



Best regards,



Anne
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