Re: [Freesurfer] failed skill strip

[Bruce Fischl]

Hi Dana,

have you checked the tal xform?

Bruce
On Wed, 5 Aug 2009, Dana W. Moore wrote:

> Hi,
>
> I have tried to run recon-all on an image and received the following error:
>
> "White matter intensity 0 is lower than CSF intensity 19. Please
> examine input images. Will terminate...
>
> MRIstripSkull failed.
>
> The T1 images look fine, and I have run several similar brains with
> no problem.  This is the first time this has happened. I am using
> version 4.4.0.  Any thoughts on what the problem is?
>
> Thanks,
> Dana
>
>
>
> Dana W. Moore, Ph.D.
> Neuropsychology Fellow
> Cornell Neuropsychology Service
> Weill Medical College of Cornell University
> New York Presbyterian Hospital
> Department of Neurology & Neuroscience
> 428 East 72nd Street, Suite 500
> New York, NY 10021
> Phone: 212-746-2441
> Fax: 212-746-5584
> Email: dwm2...@med.cornell.edu
>
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>
>
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Re: [Freesurfer] failed skill strip

[Sita Kakunoori]

Hi Dana,

Does the talairach registration look okay.
And how do orig.mgz/nu.mgz look.

Sita.



On Wed, 5 Aug 2009, Dana W. Moore wrote:

> Hi,
>
> I have tried to run recon-all on an image and received the following error:
>
> "White matter intensity 0 is lower than CSF intensity 19. Please
> examine input images. Will terminate...
>
> MRIstripSkull failed.
>
> The T1 images look fine, and I have run several similar brains with
> no problem.  This is the first time this has happened. I am using
> version 4.4.0.  Any thoughts on what the problem is?
>
> Thanks,
> Dana
>
>
>
> Dana W. Moore, Ph.D.
> Neuropsychology Fellow
> Cornell Neuropsychology Service
> Weill Medical College of Cornell University
> New York Presbyterian Hospital
> Department of Neurology & Neuroscience
> 428 East 72nd Street, Suite 500
> New York, NY 10021
> Phone: 212-746-2441
> Fax: 212-746-5584
> Email: dwm2...@med.cornell.edu
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] failed skill strip

[Dana W. Moore]

Hi,

I have tried to run recon-all on an image and received the following error:

"White matter intensity 0 is lower than CSF intensity 19. Please 
examine input images. Will terminate...

MRIstripSkull failed.

The T1 images look fine, and I have run several similar brains with 
no problem.  This is the first time this has happened. I am using 
version 4.4.0.  Any thoughts on what the problem is?

Thanks,
Dana



Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Presbyterian Hospital
Department of Neurology & Neuroscience
428 East 72nd Street, Suite 500
New York, NY 10021
Phone: 212-746-2441
Fax: 212-746-5584
Email: dwm2...@med.cornell.edu

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Re: [Freesurfer] modifying dicom headers

[Michael Harms]

You might want to check out the "DicomBrowser" as well, which can change
many files at a time (e.g., for an individual subject), although I don't
know if it can be made scriptable.

http://nrg.wustl.edu/projects/DICOM/DicomBrowser.jsp

cheers,
Mike H.

On Wed, 2009-08-05 at 15:31 -0400, Chris Watson wrote:
> dcmtk works pretty well and is easy to use:
> http://dicom.offis.de/dcmtk.php.en
> 
> Jared Price wrote:
> > Hi all,
> > I am looking for a powerful, robust tool for modifying dicom headers 
> > that can be called from the command-line and scripted.  For example, I 
> > may need to alter the subject ID with which a dicom study was uploaded.  
> > We are managing a multi-site study and the various sites do not always 
> > uplaoded the images with the correct study-wide ID.   Anyone know of a 
> > good one?
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >   
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Re: [Freesurfer] contrast matrix question

[Michael Harms]

Just to clarify what exactly do you mean by "interaction"?
("interaction" is a somewhat nebulous term, as indicated by Doug's and
mine differing responses).

If you want to look for a difference in slopes of two main continuous
effects, then a contrast vector can indeed be set up to handle that (as
noted by Doug).

If by interaction you mean the product of two continuous main effects,
then that needs to be coded into the design matrix, and the caveats that
I mentioned become applicable.

cheers,
Mike H.


On Wed, 2009-08-05 at 15:10 -0500, Michael Harms wrote:
> Hi Tori,
> There is no way to investigate the interaction of two continuous effects
> with the contrast vector alone, if the design matrix itself only
> involves main effect terms.  The interaction itself needs to be coded
> into the design matrix.
> 
> Note that it can become tricky as to the proper coefficients to use for
> the contrast vector when you have both main effect and interaction terms
> in your design matrix.  (There are in fact different "types" of
> statistics that can be estimated, and you want your contrast vector to
> be an "estimable" function.  Sophisticated statistical packages check
> that this estimability constraint is satisfied, but I suspect that
> mri_glmfit does not).
> 
> e.g.,
> http://support.sas.com/onlinedoc/913/docMainpage.jsp
> 
> cheers,
> Mike H.
> 
> 
> On Wed, 2009-08-05 at 15:48 -0400, Victoria Williams wrote:
> > Hello,
> > 
> > I apologize if this is a very simple question, but how would you set up a 
> > contrast matrix to look at the interaction of 2 variables on a measure? 
> > For example, my fsgd file contains:
> > 
> > class=1
> > variables=2
> > Input Subjid class var1 var2
> > 
> > When I tried using a contrast of 0_1_1 the significance map looks very 
> > similar to the glm run only containing var1 (contrast_0_1). I thought 
> > 0_1_1 was correct, but now I'm not so sure and would like to double check. 
> > What I am interested in is how the interaction of var1 and var2 is 
> > correlated with the brain measure per voxel. Is this possible with 
> > mri_glmfit?
> > 
> > I've checked the tutorials and scoured the internet as not to ask any
> > silly questions, but I'm having trouble finding anything helpful.
> > 
> > Thanks in advance!
> > Tori
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] contrast matrix question

[Douglas N Greve]

Oops, Mike is right, disregard my previous email.

doug

Michael Harms wrote:
> Hi Tori,
> There is no way to investigate the interaction of two continuous effects
> with the contrast vector alone, if the design matrix itself only
> involves main effect terms.  The interaction itself needs to be coded
> into the design matrix.
>
> Note that it can become tricky as to the proper coefficients to use for
> the contrast vector when you have both main effect and interaction terms
> in your design matrix.  (There are in fact different "types" of
> statistics that can be estimated, and you want your contrast vector to
> be an "estimable" function.  Sophisticated statistical packages check
> that this estimability constraint is satisfied, but I suspect that
> mri_glmfit does not).
>
> e.g.,
> http://support.sas.com/onlinedoc/913/docMainpage.jsp
>
> cheers,
> Mike H.
>
>
> On Wed, 2009-08-05 at 15:48 -0400, Victoria Williams wrote:
>   
>> Hello,
>>
>> I apologize if this is a very simple question, but how would you set up a 
>> contrast matrix to look at the interaction of 2 variables on a measure? 
>> For example, my fsgd file contains:
>>
>> class=1
>> variables=2
>> Input Subjid class var1 var2
>>
>> When I tried using a contrast of 0_1_1 the significance map looks very 
>> similar to the glm run only containing var1 (contrast_0_1). I thought 
>> 0_1_1 was correct, but now I'm not so sure and would like to double check. 
>> What I am interested in is how the interaction of var1 and var2 is 
>> correlated with the brain measure per voxel. Is this possible with 
>> mri_glmfit?
>>
>> I've checked the tutorials and scoured the internet as not to ask any
>> silly questions, but I'm having trouble finding anything helpful.
>>
>> Thanks in advance!
>> Tori
>> ___
>> Freesurfer mailing list
>> 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

In order to help us help you, please follow the steps in:
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Re: [Freesurfer] contrast matrix question

[Michael Harms]

Hi Tori,
There is no way to investigate the interaction of two continuous effects
with the contrast vector alone, if the design matrix itself only
involves main effect terms.  The interaction itself needs to be coded
into the design matrix.

Note that it can become tricky as to the proper coefficients to use for
the contrast vector when you have both main effect and interaction terms
in your design matrix.  (There are in fact different "types" of
statistics that can be estimated, and you want your contrast vector to
be an "estimable" function.  Sophisticated statistical packages check
that this estimability constraint is satisfied, but I suspect that
mri_glmfit does not).

e.g.,
http://support.sas.com/onlinedoc/913/docMainpage.jsp

cheers,
Mike H.


On Wed, 2009-08-05 at 15:48 -0400, Victoria Williams wrote:
> Hello,
> 
> I apologize if this is a very simple question, but how would you set up a 
> contrast matrix to look at the interaction of 2 variables on a measure? 
> For example, my fsgd file contains:
> 
> class=1
> variables=2
> Input Subjid class var1 var2
> 
> When I tried using a contrast of 0_1_1 the significance map looks very 
> similar to the glm run only containing var1 (contrast_0_1). I thought 
> 0_1_1 was correct, but now I'm not so sure and would like to double check. 
> What I am interested in is how the interaction of var1 and var2 is 
> correlated with the brain measure per voxel. Is this possible with 
> mri_glmfit?
> 
> I've checked the tutorials and scoured the internet as not to ask any
> silly questions, but I'm having trouble finding anything helpful.
> 
> Thanks in advance!
> Tori
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] contrast matrix question

[Douglas N Greve]

0 1 1 will just be the mean of the slopes of var1 and var2. Looks like 
you want 0 1 -1 to look for the interaction.

doug

Victoria Williams wrote:
> Hello,
>
> I apologize if this is a very simple question, but how would you set up a 
> contrast matrix to look at the interaction of 2 variables on a measure? 
> For example, my fsgd file contains:
>
> class=1
> variables=2
> Input Subjid class var1 var2
>
> When I tried using a contrast of 0_1_1 the significance map looks very 
> similar to the glm run only containing var1 (contrast_0_1). I thought 
> 0_1_1 was correct, but now I'm not so sure and would like to double check. 
> What I am interested in is how the interaction of var1 and var2 is 
> correlated with the brain measure per voxel. Is this possible with 
> mri_glmfit?
>
> I've checked the tutorials and scoured the internet as not to ask any
> silly questions, but I'm having trouble finding anything helpful.
>
> Thanks in advance!
> Tori
> ___
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> 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

In order to help us help you, please follow the steps in:
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[Freesurfer] contrast matrix question

[Victoria Williams]

Hello,

I apologize if this is a very simple question, but how would you set up a 
contrast matrix to look at the interaction of 2 variables on a measure? 
For example, my fsgd file contains:

class=1
variables=2
Input Subjid class var1 var2

When I tried using a contrast of 0_1_1 the significance map looks very 
similar to the glm run only containing var1 (contrast_0_1). I thought 
0_1_1 was correct, but now I'm not so sure and would like to double check. 
What I am interested in is how the interaction of var1 and var2 is 
correlated with the brain measure per voxel. Is this possible with 
mri_glmfit?

I've checked the tutorials and scoured the internet as not to ask any
silly questions, but I'm having trouble finding anything helpful.

Thanks in advance!
Tori
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Re: [Freesurfer] modifying dicom headers

[Chris Watson]

dcmtk works pretty well and is easy to use:
http://dicom.offis.de/dcmtk.php.en

Jared Price wrote:
> Hi all,
> I am looking for a powerful, robust tool for modifying dicom headers 
> that can be called from the command-line and scripted.  For example, I 
> may need to alter the subject ID with which a dicom study was uploaded.  
> We are managing a multi-site study and the various sites do not always 
> uplaoded the images with the correct study-wide ID.   Anyone know of a 
> good one?
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>   
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[Freesurfer] modifying dicom headers

[Jared Price]

Hi all,
I am looking for a powerful, robust tool for modifying dicom headers 
that can be called from the command-line and scripted.  For example, I 
may need to alter the subject ID with which a dicom study was uploaded.  
We are managing a multi-site study and the various sites do not always 
uplaoded the images with the correct study-wide ID.   Anyone know of a 
good one?
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Re: [Freesurfer] tksurfer display

[Pedro Paulo de Magalhães Oliveira Junior]

Two procedures may help you:
1) setenv doublebufferflag 1

2) If you virtual machine is VirtualBox, upgrade to 3.0 and enable OpenGL

---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- New Netfilter 3.2 www.Netfilter.com.br
--- New Netfilter Small Business



2009/8/5 Jerome Sallet 

> Help,
> Sorry to bother you, but I am looking for my
> tksurfer hero! I just installed freesurfer on my laptop (centos5
> virtual machine, 4Go RAM, NIVDIA quadro 110M, intel duo t2...@1.66ghz).
> Everything goes well until I tried tksurfer. Only the anterior part of
> bert's brain is displayed.(medit is ok; refreshing the
> tksurfer view doesn't change the display).
> Is there a way to fix my
> problem or is my graphic card not performant enough ?
> Thanks a lot for your help
> Cheers,
> J
>
> --
> __
> Jerome SALLET
>
> Decision and Action Laboratory
>
> Department of Experimental Psychology,
> University of Oxford
>
> South Parks Road, OX1 3UD,UK
>
> Tel (office): (0044) 1865 271 315
> Tel (elsewhere) : (0044) 7 530 060 839
>
>
> http://psyweb.psy.ox.ac.uk/rushworth/default.htm
>
>
>
>
>
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Re: [Freesurfer] Measuring the Volume of a 3D Mask

[Douglas N Greve]

The easiest way is to align the brain.mgz to mni152 with flirt, then 
apply the inverse transform

Nasim Maleki wrote:
> Dear all,
>
> I have 3D masks defined in MNI space using FSL. I would like to  
> transform these masks to each subjects anatomical space in FreeSurfer  
> and measure the volumes corresponding to these masks. Should I just  
> count the number of voxels in each mask after transformation to the  
> structural space and report the #voxels x (1x1x1mm3) as the  
> corresponding volume to that mask?
>
> Thanks for your help,
> Nasim
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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

In order to help us help you, please follow the steps in:
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[Freesurfer] tksurfer display

[Jerome Sallet]

Help,
Sorry to bother you, but I am looking for my
tksurfer hero! I just installed freesurfer on my laptop (centos5
virtual machine, 4Go RAM, NIVDIA quadro 110M, intel duo t2...@1.66ghz).
Everything goes well until I tried tksurfer. Only the anterior part of
bert's brain is displayed.(medit is ok; refreshing the
tksurfer view doesn't change the display).
Is there a way to fix my
problem or is my graphic card not performant enough ?
Thanks a lot for your help
Cheers,
J

-- 
__
Jerome SALLET

Decision and Action Laboratory

Department of Experimental Psychology,
University of Oxford

South Parks Road, OX1 3UD,UK

Tel (office): (0044) 1865 271 315
Tel (elsewhere) : (0044) 7 530 060 839


http://psyweb.psy.ox.ac.uk/rushworth/default.htm





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[Freesurfer] Measuring the Volume of a 3D Mask

[Nasim Maleki]

Dear all,

I have 3D masks defined in MNI space using FSL. I would like to  
transform these masks to each subjects anatomical space in FreeSurfer  
and measure the volumes corresponding to these masks. Should I just  
count the number of voxels in each mask after transformation to the  
structural space and report the #voxels x (1x1x1mm3) as the  
corresponding volume to that mask?

Thanks for your help,
Nasim
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Re: [Freesurfer] Cluster size threshold for the sig.mgh file

[Douglas N Greve]

Use the --minarea option

doug

Jürgen Hänggi wrote:
> Dear FS experts
>
> We would like to threshold the cluster size in the sig.mgh image in order to
> exclude clusters that are only a few vertices in size, but I cannot find
> this option
>
> Is it possible to do it within FS? If yes, how to do it?
>
> Thanks in advance
> Regards
> Jürgen
>
> 
> Juergen Haenggi
> Ph.D. (Dr. des.)
> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
>
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
> material in this e-mail is strictly forbidden.
> 
>
>
>
>
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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

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Re: [Freesurfer] ascii file

[Douglas N Greve]

The output is not a curvature file, it is a surface.

doug

Feng-Xian Yan wrote:
>
> Hi,
>
> I try again with you said. First, I type this command“mri_surf2surf
> --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv
> --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv
> --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert
> -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”.
>
> But, the error is the same.” MRISreadBinaryCurvature: incompatible
> vertex number in file ./lh.noise0.5_0_tal.xfm”
>
>
> What’s wrong? Would you help me to resolve this problem? Because I
> really want to obtain the thickness ascii file with Tal coordinate.
> Or, have you another method to obtain the thickness ascii file with
> Tal coordinate?
>
> Thank you in advance!
>
> Feng-Xian
>
>
>
> 2009/8/4 Bruce Fischl  >
>
> you need to tell it what format to write the output in. Try using -
> --tfmt curv
>
> I would have thought you needed --sfmt curv also. I'm just
> guessing though. Doug is the expert on this.
>
> cheers,
> Bruce
>
>
>
> On Tue, 4 Aug 2009, Feng-Xian Yan wrote:
>
> Hi,
>
> I had asked two problems before; one is what is coordinates when I
> type mris_convert
> -c lh.thickness lh.white lh.thickness.asc, and another is if
> the asc file
> doesn't use Tal coordinate, what commands do I type to obtain
> the thickness
> asc with Tal coordinate?, and then you responded me with ?the
> coordinates
> are native RAS. You can use mri_surf2surf to convert the
> surface to tal
> coords with the talairach.xfm.?
>
>
>
> So, first, I change the native RAS cooridinate to Tal
> coordinate with
> ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness
> --trgsubject
> noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh
> --sval-tal-xyz orig
> --tval-xyz?
>
> srcsubject = noise0.5_0
> srcval = thickness
> srctype =
> trgsubject = noise0.5_0
> trgval = noise0.5_0_tal.xfm
> trgtype =
> surfreg = sphere.reg
> srchemi = lh
> trghemi = lh
> frame = 0
> fwhm-in = 0
> fwhm-out = 0
> Reading source surface reg
> 
> /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg
> Loading source data
> Reading surface file
> 
> /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig
> Applying MNI305 talairach transform
> 0.966 0.002 -0.004 0.426;
> 0.018 0.989 0.041 -19.382;
> -0.006 0.032 0.962 17.438;
> 0.000 0.000 0.000 1.000;
> INFO: surfcluster: NOT fixing group surface area
> INFO: trgsubject = srcsubject
> Saving target data
>
>
>
> Then, I obtain the thickness asc file with Tal coordinate
> using this command
> ?mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc?
>
>
>
> But, this has an error:
>
> MRISreadBinaryCurvature: incompatible vertex number in file
> ./lh.noise0.5_0_tal.xfm
>
>
> What?s wrong? Would you tell me how to resolve?
>
>
>
> Thank you in advance!
>
>
>
> Feng-Xian
>
>
> 
>
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gr...@nmr.mgh.harvard.edu
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[Freesurfer] FW: "redraw failed: no gl window open" problem

[Guang Zeng]

Thanks a lot, I have tried this one. It does not work. 

I knew someone can solve this problem on a local machine by extracting a NVidia 
driver files and copying it to somewhere to overwrite some original OpenGL  
files. But I do not want to do this procedure on each computer in our labs. 



From: p...@netfilter.com.br
Date: Wed, 5 Aug 2009 11:21:43 -0300
Subject: Re: [Freesurfer] "redraw failed: no gl window open" problem
To: freesurfer...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu

setenv doublebufferflag=0tksurfer bert lh 
inflated---
Pedro Paulo de M. Oliveira Junior




2009/8/5 Guang Zeng 







Hi, there,

I am running the tksurfer command to view the cortical surface data as tksurfer 
bert lh inflated. But I met a problem. 
I only can view a sliver part of the brain. This sliver portion can rotate and 
do everything that tksurfer is supposed to do, 


but I can't view any more of the brain than a tiny piece. Tkmedit works fine. 

When I run the command, it gave me something like this:

surfer: current subjects dir: 
/home/m047599/freesurfer-install/freesurfer/subjects


surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/m047599/freesurfer-install/freesurfer
surfer: Reading header info from 
/home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz


surfer: vertices=131369, faces=262734
Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(bert)


surfer: using interface 
/home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl


Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...




I searched the previous posts, it looks like somebody have the same problem. 
There is no NVidia and native Linux system on my computer. I run tksurfer on a 
virtual Linux machine using NX 3. 3. 0. 6.
I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX.


I ran the glxgrears, it works, although very slow.

So, how can I solve this problem, any suggestions are highly appreciated.

Thanks a lot!

Guang  

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Re: [Freesurfer] "redraw failed: no gl window open" problem

[Pedro Paulo de Magalhães Oliveira Junior]

setenv doublebufferflag=0tksurfer bert lh inflated
---
Pedro Paulo de M. Oliveira Junior



2009/8/5 Guang Zeng 

>  Hi, there,
>
> I am running the tksurfer command to view the cortical surface data as 
> *tksurfer
> bert lh inflated*. But I met a problem.
> I only can view a sliver part of the brain. This sliver portion can rotate
> and do everything that tksurfer is supposed to do,
> but I can't view any more of the brain than a tiny piece. Tkmedit works
> fine.
>
> When I run the command, it gave me something like this:
>
> surfer: current subjects dir:
> /home/m047599/freesurfer-install/freesurfer/subjects
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /home/m047599/freesurfer-install/freesurfer
> surfer: Reading header info from
> /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz
> surfer: vertices=131369, faces=262734
> Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt
> surfer: ### redraw failed: no gl window open
> surfer: single buffered window
> surfer: tkoInitWindow(bert)
> surfer: using interface
> /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl
> Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl
> Reading
> /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl
> Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl
> Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl
> Successfully parsed tksurfer.tcl
> reading white matter vertex locations...
>
>
> I searched the previous posts, it looks like somebody have the same
> problem.
> There is no NVidia and native Linux system on my computer. I run tksurfer
> on a virtual Linux machine using NX 3. 3. 0. 6.
> I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX.
> I ran the glxgrears, it works, although very slow.
>
> So, how can I solve this problem, any suggestions are highly appreciated.
>
> Thanks a lot!
>
> Guang
>
> --
> Get free photo software from Windows Live Click 
> here.
>
> ___
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>
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[Freesurfer] "redraw failed: no gl window open" problem

[Guang Zeng]

Hi, there,

I am running the tksurfer command to view the cortical surface data as tksurfer 
bert lh inflated. But I met a problem. 
I only can view a sliver part of the brain. This sliver portion can rotate and 
do everything that tksurfer is supposed to do, 
but I can't view any more of the brain than a tiny piece. Tkmedit works fine. 

When I run the command, it gave me something like this:

surfer: current subjects dir: 
/home/m047599/freesurfer-install/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/m047599/freesurfer-install/freesurfer
surfer: Reading header info from 
/home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz
surfer: vertices=131369, faces=262734
Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(bert)
surfer: using interface 
/home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...


I searched the previous posts, it looks like somebody have the same problem. 
There is no NVidia and native Linux system on my computer. I run tksurfer on a 
virtual Linux machine using NX 3. 3. 0. 6.
I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX.
I ran the glxgrears, it works, although very slow.

So, how can I solve this problem, any suggestions are highly appreciated.

Thanks a lot!

Guang  

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