date:20080520

Re: [Freesurfer] missing libg2c.0.dylib

2008-05-20 Thread Nick Schmansky

I'll see if I can get future builds to use the static lib, so as the
libg2c.dylib installation isn't required.


On Tue, 2008-05-20 at 21:34 -0300, Pedro Paulo de Magalhães Oliveira
Junior wrote:
> I had the same problem with 4.0.4
>  
> The solution is:
>  
> Install G77 (Fortran). Link:
> http://prdownloads.sourceforge.net/hpc/g77-intel-bin.tar.gz?download
>  
> Regards,
>  
> PPJ
> 
> 
> 2008/5/20 Nick Schmansky <[EMAIL PROTECTED]>:
> Jose,
> 
> Which distribution did you install?  You can find out by
> typing:
> 
> cat $FREESURFER_HOME/build-stamp.txt
> 
> You should have the leopard intel mac distribution, so it
> should say:
> 
>  freesurfer-Darwin-leopard-i686-stable-v4.0.4
> 
> Also make sure you have all the latest Apple Software Updates.
> 
> Nick
> 
> 
> 
> On Tue, 2008-05-20 at 19:33 -0400, Jose Miguel Selman wrote:
> > Hi everyone:
> >
> > I have run freesurfer on Centos for a while now with no
> problems. I
> > installed the most recent version on a MacBook pro. Tkmedit
> and
> > Tksurfer work fine, but when attempting the recon-all
> processing I get
> > an error of a "missing libg2c.0.dylib". The last part of the
> log
> > follows:
> >
> >
> -
> > gauss_4dfp talsrcimg 1.1
> >
> -
> >
> > dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib
> >Referenced from: /Applications/freesurfer/bin/gauss_4dfp
> >Reason: image not found
> > Trace/BPT trap
> > ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
> > ERROR: mpr2mni305 execution aborted
> > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> > Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin
> Kernel
> > Version 9.2.2: Tue Mar  4 21:17:34 PST 2008;
> root:xnu-1228.4.31~1/
> > RELEASE_I386 i386
> >
> > recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4
> 2008
> >
> >
> >
> >
> > I tried to get information on the list but could not find
> anything.
> >
> > Thanks
> > Dr. Jose M Selman
> >
> >
> > Confidencialidad:
> > La informacion contenida en este correo y cualquier archivo
> adjunto es de caracter confidencial. La utilizacion,
> distribucion, divulgacion o reproduccion esta autorizada
> exclusivamente para su(s) destinatario(s). Si ha recibido este
> correo por error, por favor notifiquelo a su remitente y
> eliminelo completamente de sus recipientes. Clinica Las Condes
> se lo agradece.(Los acentos han sido suprimidos
> intencionalmente para no exponer al texto a reemplazos de los
> caracteres acentuados.)
> >  The information contained in this e-mail and any attached
> files is strictly confidential. Its use, distribution,
> publication or reproduction is exclusively authorized for its
> addressee.  If you have received it by error, please notify
> its sender and eliminate it completely from your files.
> Clinica Las Condes thanks you.
> >
> > ___
> > 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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[Freesurfer] a problem

2008-05-20 Thread yczhang

Using lgi or thickness,how could I know the anatomical correspondence for a  
statistical difference area which had been found between patients and controls. 
I have to report the significant regions ,for example ,postcentral sulcus or 
posterior cingulate
Thanks!




yczhang
2008-05-21
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[Freesurfer] a problem

2008-05-20 Thread yczhang

Using lgi or thickness,how could I know the anatomical correspondence for a  
statistical difference area which had been found between patients and controls.
Thanks!




yczhang
2008-05-21
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Re: [Freesurfer] missing libg2c.0.dylib

2008-05-20 Thread Jose Miguel Selman

That solved my problem. Processing like a bullet well ahead of my  
previous problem.

Thanks PPJ

Jose Miguel Selman

On May 20, 2008, at 8:34 PM, Pedro Paulo de Magalhães Oliveira Junior  
wrote:

I had the same problem with 4.0.4

The solution is:

Install G77 (Fortran). Link: 
http://prdownloads.sourceforge.net/hpc/g77-intel-bin.tar.gz?download

Regards,

PPJ

2008/5/20 Nick Schmansky <[EMAIL PROTECTED]>:
Jose,

Which distribution did you install?  You can find out by typing:

cat $FREESURFER_HOME/build-stamp.txt

You should have the leopard intel mac distribution, so it should say:

 freesurfer-Darwin-leopard-i686-stable-v4.0.4

Also make sure you have all the latest Apple Software Updates.

Nick

On Tue, 2008-05-20 at 19:33 -0400, Jose Miguel Selman wrote:
> Hi everyone:
>
> I have run freesurfer on Centos for a while now with no problems. I
> installed the most recent version on a MacBook pro. Tkmedit and
> Tksurfer work fine, but when attempting the recon-all processing I  
get

> an error of a "missing libg2c.0.dylib". The last part of the log
> follows:
>
>  
-

> gauss_4dfp talsrcimg 1.1
>  
-

>
> dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib
>Referenced from: /Applications/freesurfer/bin/gauss_4dfp
>Reason: image not found
> Trace/BPT trap
> ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
> ERROR: mpr2mni305 execution aborted
> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin Kernel
> Version 9.2.2: Tue Mar  4 21:17:34 PST 2008; root:xnu-1228.4.31~1/
> RELEASE_I386 i386
>
> recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4 2008
>
>
>
>
> I tried to get information on the list but could not find anything.
>
> Thanks
> Dr. Jose M Selman
>
>
> Confidencialidad:
> La informacion contenida en este correo y cualquier archivo  
adjunto es de caracter confidencial. La utilizacion, distribucion,  
divulgacion o reproduccion esta autorizada exclusivamente para su(s)  
destinatario(s). Si ha recibido este correo por error, por favor  
notifiquelo a su remitente y eliminelo completamente de sus  
recipientes. Clinica Las Condes se lo agradece.(Los acentos han sido  
suprimidos intencionalmente para no exponer al texto a reemplazos de  
los caracteres acentuados.)
>  The information contained in this e-mail and any attached files  
is strictly confidential. Its use, distribution, publication or  
reproduction is exclusively authorized for its addressee.  If you  
have received it by error, please notify its sender and eliminate it  
completely from your files. Clinica Las Condes thanks you.

>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Confidencialidad:
La informacion contenida en este correo y cualquier archivo adjunto es de 
caracter confidencial. La utilizacion, distribucion, divulgacion o reproduccion 
esta autorizada exclusivamente para su(s) destinatario(s). Si ha recibido este 
correo por error, por favor notifiquelo a su remitente y eliminelo 
completamente de sus recipientes. Clinica Las Condes se lo agradece.(Los 
acentos han sido suprimidos intencionalmente para no exponer al texto a 
reemplazos de los caracteres acentuados.)
The information contained in this e-mail and any attached files is strictly 
confidential. Its use, distribution, publication or reproduction is exclusively 
authorized for its addressee.  If you have received it by error, please notify 
its sender and eliminate it completely from your files. Clinica Las Condes 
thanks you.
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Re: [Freesurfer] missing libg2c.0.dylib

2008-05-20 Thread Pedro Paulo de Magalhães Oliveira Junior

I had the same problem with 4.0.4

The solution is:

Install G77 (Fortran). Link:
http://prdownloads.sourceforge.net/hpc/g77-intel-bin.tar.gz?download

Regards,

PPJ

2008/5/20 Nick Schmansky <[EMAIL PROTECTED]>:

> Jose,
>
> Which distribution did you install?  You can find out by typing:
>
> cat $FREESURFER_HOME/build-stamp.txt
>
> You should have the leopard intel mac distribution, so it should say:
>
>  freesurfer-Darwin-leopard-i686-stable-v4.0.4
>
> Also make sure you have all the latest Apple Software Updates.
>
> Nick
>
>
> On Tue, 2008-05-20 at 19:33 -0400, Jose Miguel Selman wrote:
> > Hi everyone:
> >
> > I have run freesurfer on Centos for a while now with no problems. I
> > installed the most recent version on a MacBook pro. Tkmedit and
> > Tksurfer work fine, but when attempting the recon-all processing I get
> > an error of a "missing libg2c.0.dylib". The last part of the log
> > follows:
> >
> > -
> > gauss_4dfp talsrcimg 1.1
> > -
> >
> > dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib
> >Referenced from: /Applications/freesurfer/bin/gauss_4dfp
> >Reason: image not found
> > Trace/BPT trap
> > ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
> > ERROR: mpr2mni305 execution aborted
> > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> > Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin Kernel
> > Version 9.2.2: Tue Mar  4 21:17:34 PST 2008; root:xnu-1228.4.31~1/
> > RELEASE_I386 i386
> >
> > recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4 2008
> >
> >
> >
> >
> > I tried to get information on the list but could not find anything.
> >
> > Thanks
> > Dr. Jose M Selman
> >
> >
> > Confidencialidad:
> > La informacion contenida en este correo y cualquier archivo adjunto es de
> caracter confidencial. La utilizacion, distribucion, divulgacion o
> reproduccion esta autorizada exclusivamente para su(s) destinatario(s). Si
> ha recibido este correo por error, por favor notifiquelo a su remitente y
> eliminelo completamente de sus recipientes. Clinica Las Condes se lo
> agradece.(Los acentos han sido suprimidos intencionalmente para no exponer
> al texto a reemplazos de los caracteres acentuados.)
> >  The information contained in this e-mail and any attached files is
> strictly confidential. Its use, distribution, publication or reproduction is
> exclusively authorized for its addressee.  If you have received it by error,
> please notify its sender and eliminate it completely from your files.
> Clinica Las Condes thanks you.
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] missing libg2c.0.dylib

2008-05-20 Thread Nick Schmansky

Jose,

Which distribution did you install?  You can find out by typing:

cat $FREESURFER_HOME/build-stamp.txt

You should have the leopard intel mac distribution, so it should say:

 freesurfer-Darwin-leopard-i686-stable-v4.0.4

Also make sure you have all the latest Apple Software Updates.

Nick


On Tue, 2008-05-20 at 19:33 -0400, Jose Miguel Selman wrote:
> Hi everyone:
> 
> I have run freesurfer on Centos for a while now with no problems. I  
> installed the most recent version on a MacBook pro. Tkmedit and  
> Tksurfer work fine, but when attempting the recon-all processing I get  
> an error of a "missing libg2c.0.dylib". The last part of the log  
> follows:
> 
> -
> gauss_4dfp talsrcimg 1.1
> -
> 
> dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib
>Referenced from: /Applications/freesurfer/bin/gauss_4dfp
>Reason: image not found
> Trace/BPT trap
> ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
> ERROR: mpr2mni305 execution aborted
> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin Kernel  
> Version 9.2.2: Tue Mar  4 21:17:34 PST 2008; root:xnu-1228.4.31~1/ 
> RELEASE_I386 i386
> 
> recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4 2008
> 
> 
> 
> 
> I tried to get information on the list but could not find anything.
> 
> Thanks
> Dr. Jose M Selman
> 
> 
> Confidencialidad:
> La informacion contenida en este correo y cualquier archivo adjunto es de 
> caracter confidencial. La utilizacion, distribucion, divulgacion o 
> reproduccion esta autorizada exclusivamente para su(s) destinatario(s). Si ha 
> recibido este correo por error, por favor notifiquelo a su remitente y 
> eliminelo completamente de sus recipientes. Clinica Las Condes se lo 
> agradece.(Los acentos han sido suprimidos intencionalmente para no exponer al 
> texto a reemplazos de los caracteres acentuados.)
>  The information contained in this e-mail and any attached files is strictly 
> confidential. Its use, distribution, publication or reproduction is 
> exclusively authorized for its addressee.  If you have received it by error, 
> please notify its sender and eliminate it completely from your files. Clinica 
> Las Condes thanks you.
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 

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[Freesurfer] missing libg2c.0.dylib

2008-05-20 Thread Jose Miguel Selman


Hi everyone:

I have run freesurfer on Centos for a while now with no problems. I  
installed the most recent version on a MacBook pro. Tkmedit and  
Tksurfer work fine, but when attempting the recon-all processing I get  
an error of a "missing libg2c.0.dylib". The last part of the log  
follows:


-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib
  Referenced from: /Applications/freesurfer/bin/gauss_4dfp
  Reason: image not found
Trace/BPT trap
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
ERROR: mpr2mni305 execution aborted
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin Kernel  
Version 9.2.2: Tue Mar  4 21:17:34 PST 2008; root:xnu-1228.4.31~1/ 
RELEASE_I386 i386


recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4 2008




I tried to get information on the list but could not find anything.

Thanks
Dr. Jose M Selman


Confidencialidad:
La informacion contenida en este correo y cualquier archivo adjunto es de 
caracter confidencial. La utilizacion, distribucion, divulgacion o reproduccion 
esta autorizada exclusivamente para su(s) destinatario(s). Si ha recibido este 
correo por error, por favor notifiquelo a su remitente y eliminelo 
completamente de sus recipientes. Clinica Las Condes se lo agradece.(Los 
acentos han sido suprimidos intencionalmente para no exponer al texto a 
reemplazos de los caracteres acentuados.)
The information contained in this e-mail and any attached files is strictly 
confidential. Its use, distribution, publication or reproduction is exclusively 
authorized for its addressee.  If you have received it by error, please notify 
its sender and eliminate it completely from your files. Clinica Las Condes 
thanks you.

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Re: [Freesurfer] Question regarding computing contrasts with mri_glmfit

2008-05-20 Thread Doug Greve


yep, that looks fine.

doug

Avram Holmes wrote:


All,

I'm just looking for a little advice on constructing fsgd and .mat 
files. I would like to compare a healthy control sample with the data 
from two MDD groups. To do so I made my fsgd file to look like the 
following:


GroupDescriptorFile 1
Title MoneyGame_Subjects
Class Control
Class MDD
Class Anhedonic

Input REWARD111 Control
Input REWARD201 Anhedonic
Input REWARD207 MDD
Input REWARD208 
Anhedonic 

Input REWARD211 
MDD   

Input REWARD212 MDD   

Input REWARD213 
Anhedonic 


Input REWARD215 Anhedonic
Input REWARD277 Control
Input REWARD278 Control


This file results in a design matrix with 3 columns.

I am interested in conducting the following analyses and I wanted to 
check to see if I am coding all of the .mat files correctly.


Controls vs all Patients (1 -.5 -.5)
Anhedonic vs MDD (0 1 -1)
Controls vs Anhedonic (1 0 -1)
Controls vs MDD (1 -1 0)

Thank you in advance for any help you can offer.

Avram

--


Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall  Phone:(617) 495-0790
33 Kirkland Street   Fax:(617) 495-3728
Cambridge, MA 02138, USA Email: [EMAIL PROTECTED]




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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] Possible to regress whole-brain functional data against continuous variables in the volume?

2008-05-20 Thread Doug Greve

Hi Dan, yes it is possible. Algorithmically, it is actually no different 
than doing it in the surface. Just give mri_glmfit the functional volume 
stack instead of a surface stack.


doug

Dan Dillon wrote:

Hi FreeSurfers. Is it possible to regress functional data against a 
continuous variable in the volume? I'm analyzing a reward processing 
study that activates sub-cortical and cortical regions, and I'd like 
to regress those data against a continuous measure of depressive 
symptoms administered to each participant. I understand the basic 
fsgd/mri_glmfit approach from the FS tutorial, but I want to stay in 
the volume in order to examine sub-cortical structures (e.g., nucleus 
accumbens). Is this possible?


 


Thanks!

 


Dan Dillon, Ph.D.

Post-doctoral Fellow

Affective Neuroscience Lab

Dept. of Psychology, Harvard University

Phone: (617) 495-1889

E-mail: [EMAIL PROTECTED] 

 




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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] cannot allocate memory problem when using make average subject

2008-05-20 Thread Doug Greve



I've put the files back in that location (make_average_*). Run 
make_average_subject with --no-aseg. But I'm not sure this is the 
problem. It looks like it is failing when creating the average surface 
(the fix above is for the volume only). But give it a try. Also, 
remember to send the entire log file so we can better debug it.


doug



Jiefeng Jiang wrote:


Hi,
 
I was trying to build an average subject using 250 subjects and I got 
the following error message:
 
processing subject nor76 (246 of 250)
reading spherical surface 
/DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg...

reading colortable from annotation file...
colortable with 35 entries read (originally 
/space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)

curvature mean = -0.017, std = 0.597
curvature mean = -0.064, std = 0.640
ripping medial wall...
computing parameterization for surface 
/DATA_FREESURFER/Data/nor76/surf/rh.inflated.H...

ImageAlloc: could not allocate 512x256 buffer
 
curvature mean = -0.088, std = 0.872

Cannot allocate memory
I saw someone discussing this issue a few month ago and Doug 
provided new scripts of make_average_subject, make_average_volume and 
make_average_surface to solve this problem. However, I can't find 
these files using the link 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
Can anyone tell me whether and how this problem has been solved? 
Thanks in advance!
 
 
Jiefeng Jiang
 




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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] segmentation problem

2008-05-20 Thread Dick, Rachel

Hello,

 

I'm having some issues with the cortex as seen in the attached picture.
I know in the more medial regions I can add control points to the white
matter to help the pial line extend further out.  However, laterally,
I'm not sure how to include that cortex that is left out.  Any help
would be greatly appreciated.

 

Thanks in advance,

 

Rachel

 

 

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Re: [Freesurfer] missing libg2c.0.dylib

[Freesurfer] a problem

[Freesurfer] a problem

Re: [Freesurfer] missing libg2c.0.dylib

Re: [Freesurfer] missing libg2c.0.dylib

Re: [Freesurfer] missing libg2c.0.dylib

[Freesurfer] missing libg2c.0.dylib

Re: [Freesurfer] Question regarding computing contrasts with mri_glmfit

Re: [Freesurfer] Possible to regress whole-brain functional data against continuous variables in the volume?

Re: [Freesurfer] cannot allocate memory problem when using make average subject

[Freesurfer] segmentation problem

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