Re: [Freesurfer] Fwd: LGI path problem

2013-10-28 Thread Linn Mittlestein 
Dear Marie,

Thank you, I use bash and changed my .bashrc and this worked, I previously
had used wrong syntax. Thank you very much for your help. However, I now
recieve another error and do not know what it means at all. I copy in the
error ! Thank you.

Improper assignment with rectangular empty matrix.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!



On Wed, Oct 23, 2013 at 4:04 PM, Marie Schaer  wrote:

>
>  Hi Linn,
>
>  If you are using tcsh, you have to edit the file $HOME/.cshrc (.shrc
> should work as well) to add the following line:
>
>  setenv PATH $PATH:/YOUR_PATH_TO_MATLAB_BIN_DIRECTORY
>
>  Then close the terminal and open a new one. Use the env command to be
> sure that your path has been modified, then the getmatlab command from
> FreeSurfer should give you the correct location.
>
>  Best,
>
>  Marie
>
>
>  On Oct 23, 2013, at 12:23 AM, Linn Mittlestein 
>  wrote:
>
>  Hi, thank you. I am using Linux. I not sure where to change path, ie
> which file this should be done in and where this file is located. This the
> error message I recieve, and as I said It is launching the wrong matlab and
> I don't know how change this.
>
> Launching Matlab7p13
>
> Warning: Unable to open display 'iconic'. You will not be able to display
> graphics on the screen.
>
>  < M A T L A B (R) >
>
> Copyright 1984-2011 The MathWorks, Inc.
>
> R2011b (7.13.0.564) 32-bit (glnx86)
>
> August 13, 2011
>
>
>  To get started, type one of these: helpwin, helpdesk, or demo.
>
> For product information, visit www.mathworks.com.
>
>  >> reading filled volume...
>
> closing volume...
>
> Undefined function 'fspecial' for input arguments of type 'char'.
>
>  Error in make_outer_surface (line 31)
>
> Gaussian = fspecial('gaussian',[2 2],1);
>
>  >>
>
> ERROR: make_outer_surface did not create output file
> '/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
>
> Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64
> x86_64 x86_64 GNU/Linux
>
>  recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58 BST 2013
>
>
>  Thank you very much for your time and help,
>
>
>  Kind Regards,Linn
>
>
>
>
> On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer wrote:
>
>>
>>  Hi Linn,
>>
>>  Sorry for the delay in answering. The path has to be set directly in
>> your environment variable (the variable $PATH has to point to the correct
>> version). I need a few more details about what you tried and which OS you
>> are using to be able to help you.
>>
>>  If you are using mac, here is an example on how you can set the path in
>> the .shrc file:
>>  setenv PATH $PATH":/Applications/MATLAB_R2013b.app/bin"
>>
>>  You can also have a look at the following posts:
>>  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html
>>
>>  Let me know how it goes,
>>
>>  Marie
>>
>>
>>  On Oct 22, 2013, at 2:41 AM, Linn Mittlestein 
>>  wrote:
>>
>>Hi,
>>
>>  I am trying to compute lgi measures, and I think my problem lies in the
>> fact that the matlab path is not set correctly; it is calling an older
>> version of matlab however I need it to point to matlab2013b. I have tried
>> numerous things like changing the startup.m file, the .bashrc file and
>> exporting the matlab path, however It keeps calling another version of
>> Matlab. Can someone please tell me how exactly the path is set and where?
>>
>>  Best Wishes and thank you,
>>
>> Linn
>>
>> -- Forwarded message --
>> From: Linn Mittlestein 
>> Date: Mon, Oct 21, 2013 at 9:33 AM
>> Subject: Fwd: LGI path problem
>> To: freesurfer@nmr.mgh.harvard.edu
>>
>>
>>
>> From: Linn Mittlestein Date: Fri, Oct 18, 2013 at
>> 1:30 PM
>> Subject: LGI path problem
>> To: freesurfer@nmr.mgh.harvard.edu
>>
>>
>>
>>  Hi,
>>
>>  I am trying to compute lgi measures, and I think my problem lies in the
>> fact that the matlab path is not set correctly; it is calling an older
>> version of matlab however I need it to point to matlab2013b. I have tried
>> numerous things like changing the startup.m file, the .bashrc file and
>> exporting the matlab path, however It keeps calling another version of
>> Matlab. Can someone please tell me how exactly the path is set and where?
>>
>>  Best Wishes and thank you,
>>
>> Linn
>>
>>
>>   _

Re: [Freesurfer] Fwd: LGI path problem

2013-10-23 Thread Marie Schaer 

Hi Linn,

If you are using tcsh, you have to edit the file $HOME/.cshrc (.shrc should 
work as well) to add the following line:

setenv PATH $PATH:/YOUR_PATH_TO_MATLAB_BIN_DIRECTORY

Then close the terminal and open a new one. Use the env command to be sure that 
your path has been modified, then the getmatlab command from FreeSurfer should 
give you the correct location.

Best,

Marie


On Oct 23, 2013, at 12:23 AM, Linn Mittlestein 
mailto:linnmit...@gmail.com>>
 wrote:

Hi, thank you. I am using Linux. I not sure where to change path, ie which file 
this should be done in and where this file is located. This the error message I 
recieve, and as I said It is launching the wrong matlab and I don't know how 
change this.


Launching Matlab7p13

Warning: Unable to open display 'iconic'. You will not be able to display 
graphics on the screen.


< M A T L A B (R) >

Copyright 1984-2011 The MathWorks, Inc.

R2011b (7.13.0.564) 32-bit (glnx86)

August 13, 2011



To get started, type one of these: helpwin, helpdesk, or demo.

For product information, visit www.mathworks.com.


>> reading filled volume...

closing volume...

Undefined function 'fspecial' for input arguments of type 'char'.


Error in make_outer_surface (line 31)

Gaussian = fspecial('gaussian',[2 2],1);


>>

ERROR: make_outer_surface did not create output file 
'/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!

Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 
x86_64 x86_64 GNU/Linux


recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58 BST 2013


Thank you very much for your time and help,


Kind Regards,Linn




On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer 
mailto:marie.sch...@unige.ch>> wrote:

Hi Linn,

Sorry for the delay in answering. The path has to be set directly in your 
environment variable (the variable $PATH has to point to the correct version). 
I need a few more details about what you tried and which OS you are using to be 
able to help you.

If you are using mac, here is an example on how you can set the path in the 
.shrc file:
setenv PATH $PATH":/Applications/MATLAB_R2013b.app/bin"

You can also have a look at the following posts:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html

Let me know how it goes,

Marie


On Oct 22, 2013, at 2:41 AM, Linn Mittlestein 
mailto:linnmit...@gmail.com>>
 wrote:

Hi,

I am trying to compute lgi measures, and I think my problem lies in the fact 
that the matlab path is not set correctly; it is calling an older version of 
matlab however I need it to point to matlab2013b. I have tried numerous things 
like changing the startup.m file, the .bashrc file and exporting the matlab 
path, however It keeps calling another version of Matlab. Can someone please 
tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn

-- Forwarded message --
From: Linn Mittlestein mailto:linnmit...@gmail.com>>
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu



From: Linn Mittlestein mailto:linnmit...@gmail.com>>Date: 
Fri, Oct 18, 2013 at 1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu



Hi,

I am trying to compute lgi measures, and I think my problem lies in the fact 
that the matlab path is not set correctly; it is calling an older version of 
matlab however I need it to point to matlab2013b. I have tried numerous things 
like changing the startup.m file, the .bashrc file and exporting the matlab 
path, however It keeps calling another version of Matlab. Can someone please 
tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn


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Re: [Freesurfer] Fwd: LGI path problem

2013-10-23 Thread Linn Mittlestein 
Hi, thank you. I am using Linux. I not sure where to change path, ie which
file this should be done in and where this file is located. This the error
message I recieve, and as I said It is launching the wrong matlab and I
don't know how change this.

 Launching Matlab7p13

Warning: Unable to open display 'iconic'. You will not be able to display
graphics on the screen.

 < M A T L A B (R) >

Copyright 1984-2011 The MathWorks, Inc.

R2011b (7.13.0.564) 32-bit (glnx86)

August 13, 2011

  To get started, type one of these: helpwin, helpdesk, or demo.

For product information, visit www.mathworks.com.

 >> reading filled volume...

closing volume...

Undefined function 'fspecial' for input arguments of type 'char'.

 Error in make_outer_surface (line 31)

Gaussian = fspecial('gaussian',[2 2],1);

 >>

ERROR: make_outer_surface did not create output file
'/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!

Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64
x86_64 x86_64 GNU/Linux

 recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58 BST 2013


Thank you very much for your time and help,


Kind Regards,Linn




On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer wrote:

>
>  Hi Linn,
>
>  Sorry for the delay in answering. The path has to be set directly in
> your environment variable (the variable $PATH has to point to the correct
> version). I need a few more details about what you tried and which OS you
> are using to be able to help you.
>
>  If you are using mac, here is an example on how you can set the path in
> the .shrc file:
>  setenv PATH $PATH":/Applications/MATLAB_R2013b.app/bin"
>
>  You can also have a look at the following posts:
>  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html
>
>  Let me know how it goes,
>
>  Marie
>
>
>  On Oct 22, 2013, at 2:41 AM, Linn Mittlestein 
>  wrote:
>
>   Hi,
>
>  I am trying to compute lgi measures, and I think my problem lies in the
> fact that the matlab path is not set correctly; it is calling an older
> version of matlab however I need it to point to matlab2013b. I have tried
> numerous things like changing the startup.m file, the .bashrc file and
> exporting the matlab path, however It keeps calling another version of
> Matlab. Can someone please tell me how exactly the path is set and where?
>
>  Best Wishes and thank you,
>
> Linn
>
> -- Forwarded message --
> From: Linn Mittlestein 
> Date: Mon, Oct 21, 2013 at 9:33 AM
> Subject: Fwd: LGI path problem
> To: freesurfer@nmr.mgh.harvard.edu
>
>
>
> From: Linn Mittlestein Date: Fri, Oct 18, 2013 at
> 1:30 PM
> Subject: LGI path problem
> To: freesurfer@nmr.mgh.harvard.edu
>
>
>
>  Hi,
>
>  I am trying to compute lgi measures, and I think my problem lies in the
> fact that the matlab path is not set correctly; it is calling an older
> version of matlab however I need it to point to matlab2013b. I have tried
> numerous things like changing the startup.m file, the .bashrc file and
> exporting the matlab path, however It keeps calling another version of
> Matlab. Can someone please tell me how exactly the path is set and where?
>
>  Best Wishes and thank you,
>
> Linn
>
>
>  ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>
> 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] Fwd: LGI path problem

2013-10-22 Thread Marie Schaer 

Hi Linn,

Sorry for the delay in answering. The path has to be set directly in your 
environment variable (the variable $PATH has to point to the correct version). 
I need a few more details about what you tried and which OS you are using to be 
able to help you.

If you are using mac, here is an example on how you can set the path in the 
.shrc file:
setenv PATH $PATH":/Applications/MATLAB_R2013b.app/bin"

You can also have a look at the following posts:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html

Let me know how it goes,

Marie


On Oct 22, 2013, at 2:41 AM, Linn Mittlestein 
mailto:linnmit...@gmail.com>>
 wrote:

Hi,

I am trying to compute lgi measures, and I think my problem lies in the fact 
that the matlab path is not set correctly; it is calling an older version of 
matlab however I need it to point to matlab2013b. I have tried numerous things 
like changing the startup.m file, the .bashrc file and exporting the matlab 
path, however It keeps calling another version of Matlab. Can someone please 
tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn

-- Forwarded message --
From: Linn Mittlestein mailto:linnmit...@gmail.com>>
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu



From: Linn Mittlestein mailto:linnmit...@gmail.com>>Date: 
Fri, Oct 18, 2013 at 1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu



Hi,

I am trying to compute lgi measures, and I think my problem lies in the fact 
that the matlab path is not set correctly; it is calling an older version of 
matlab however I need it to point to matlab2013b. I have tried numerous things 
like changing the startup.m file, the .bashrc file and exporting the matlab 
path, however It keeps calling another version of Matlab. Can someone please 
tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn


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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

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[Freesurfer] Fwd: LGI path problem

2013-10-22 Thread Linn Mittlestein 
Hi,

I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
exporting the matlab path, however It keeps calling another version of
Matlab. Can someone please tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn

-- Forwarded message --
From: Linn Mittlestein 
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu



From: Linn Mittlestein Date: Fri, Oct 18, 2013 at
1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu



Hi,

I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
exporting the matlab path, however It keeps calling another version of
Matlab. Can someone please tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Fwd: LGI path problem

2013-10-21 Thread Linn Mittlestein 
From: Linn Mittlestein Date: Fri, Oct 18, 2013 at
1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu


Hi,

I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
exporting the matlab path, however It keeps calling another version of
Matlab. Can someone please tell me how exactly the path is set and where?

Best Wishes and thank you,

Linn
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.