subject:"\[Freesurfer\] License problem"

Re: [Freesurfer] License problem

2016-12-16 Thread Bruce Fischl

if recon-all works then you must have a license file. Are you sure that 
FREESURFER_HOME is defined in your environment and points to the right 
place? That's where we look for the license file (then in 
/Applications/freesurfer on the mac if FREESURFER_HOME isn't defined in 
the env0


cheers
Bruce
On Fri, 16 Dec 2016, Marco Ganzetti wrote:


At the current stage I can run recon-all and get the results without
problems.
If the license would not work I couldn't be able to run it.

Can someone send me the type of license file I should generate?
In the website it says that I should get a license.txt by email, but I
didn't get any file just instructions how to create a new file or modify the
existing LICENSE file.



Marco Ganzetti, PhD

Il 16 Dic 2016 19:47, Z K  ha scritto:
  Is the file you created located in /Applications/freesurfer?

  Also, fir good measure, try creating the same file but naming it
  .license in the /Applications/freesurfer

  On 12/16/2016 11:20 AM, Marco Ganzetti wrote:
  > Dear all,
  > I am trying to display a volumetric file to a surface using
  mri_vol2surf
  > and then tksurfer.
  > Here is the error message I get.
  >
  > I have obtained the email with the few license lines to copy
  in a file
  > (that i created) name license.txt
  > I created a new file and erased the existing LICENSE
  >
  > Thanks
  > Marco Ganzetti
  >
  > Last login: Fri Dec 16 16:56:54 on ttys002
  >  freesurfer-Darwin-lion-stable-pub-v5.3.0 
  > Setting up environment for FreeSurfer/FS-FAST (and FSL)
  > FREESURFER_HOME   /Applications/freesurfer
  > FSFAST_HOME   /Applications/freesurfer/fsfast
  > FSF_OUTPUT_FORMAT nii.gz
  > SUBJECTS_DIR  /Applications/freesurfer/subjects
  > MNI_DIR   /Applications/freesurfer/mni
  > FSL_DIR   /usr/local/fsl
  > Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile
  >  freesurfer-Darwin-lion-stable-pub-v5.3.0 
  > Setting up environment for FreeSurfer/FS-FAST (and FSL)
  > FREESURFER_HOME   /Applications/freesurfer
  > FSFAST_HOME   /Applications/freesurfer/fsfast
  > FSF_OUTPUT_FORMAT nii.gz
  > SUBJECTS_DIR  /Applications/freesurfer/subjects
  > MNI_DIR   /Applications/freesurfer/mni
  > FSL_DIR   /usr/local/fsl
  > Binds-MacBook-Pro:~ Marco$ export
  > SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN
  > Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src
  >
  /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
  > --regheader elab --hemi lh --o
  >
  /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
  > srcvol =
  /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
  > srcreg unspecified
  > srcregold = 0
  > srcwarp unspecified
  > surf = white
  > hemi = lh
  > reshape = 0
  > interp = nearest
  > float2int = round
  > GetProjMax = 0
  > INFO: float2int code = 0
  > Done loading volume
  > Computing registration from header.
  >   Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
  as target
  > reference.
  > Reading surface
  /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white
  > Done reading source surface
  > Mapping Source Volume onto Source Subject Surface
  >  1 0 0 0
  > using old
  > Done mapping volume to surface
  > Number of source voxels hit = 41923
  > Writing to
  >
  /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
  > Dim: 116772 1 1
  > Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay
  >
  /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
  > subject is elab
  > hemi    is lh
  > surface is inflated
  > surfer: current subjects dir:
  /Users/Marco/Desktop/surface_RORDEN
  > surfer: not in "scripts" dir ==> using cwd for session root
  > surfer: session root data dir ($session) set to:
  > surfer: /Users/Marco
  > checking for nofix files in 'inflated'
  > Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab)
  > Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
  > surfer: Reading header info from
  > /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
  >
  --
  > ERROR: FreeSurfer license file
  /Applications/freesurfer/.license not found.
  >   If you are outside the NMR-Martinos Center,
  >   go to http://surfer.nmr.mgh.harvard.edu to
  >   get a valid license file (it's free).
  >   If you are inside the NMR-Martinos Center,
  >   make sure to source the standard environment.
  >

Re: [Freesurfer] License problem

2016-12-16 Thread Marco Ganzetti

At the current stage I can run recon-all and get the results without problems.

If the license would not work I couldn't be able to run it.

Can someone send me the type of license file I should generate?
In the website it says that I should get a license.txt by email, but I didn't 
get any file just instructions how to create a new file or modify the existing 
LICENSE file.



Marco Ganzetti, PhD

Il 16 Dic 2016 19:47, Z K  ha scritto:
Is the file you created located in /Applications/freesurfer?

Also, fir good measure, try creating the same file but naming it
.license in the /Applications/freesurfer

On 12/16/2016 11:20 AM, Marco Ganzetti wrote:
> Dear all,
> I am trying to display a volumetric file to a surface using mri_vol2surf
> and then tksurfer.
> Here is the error message I get.
>
> I have obtained the email with the few license lines to copy in a file
> (that i created) name license.txt
> I created a new file and erased the existing LICENSE
>
> Thanks
> Marco Ganzetti
>
> Last login: Fri Dec 16 16:56:54 on ttys002
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
> Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
> Binds-MacBook-Pro:~ Marco$ export
> SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN
> Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
> --regheader elab --hemi lh --o
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
> srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>   Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target
> reference.
> Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 41923
> Writing to
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
> Dim: 116772 1 1
> Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
> subject is elab
> hemiis lh
> surface is inflated
> surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /Users/Marco
> checking for nofix files in 'inflated'
> Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab)
> Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
> surfer: Reading header info from
> /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> Binds-MacBook-Pro:~ Marco$
>
> - - -
>
> *Marco Ganzetti, PhD*
>
> Movement Control & Neuroplasticity Research Group
> Tervuursevest 101, 3001 Leuven
>
> email: marco.ganze...@kuleuven.be 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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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
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Re: [Freesurfer] License problem

2016-12-16 Thread Z K

Is the file you created located in /Applications/freesurfer?

Also, fir good measure, try creating the same file but naming it 
.license in the /Applications/freesurfer

On 12/16/2016 11:20 AM, Marco Ganzetti wrote:
> Dear all,
> I am trying to display a volumetric file to a surface using mri_vol2surf
> and then tksurfer.
> Here is the error message I get.
>
> I have obtained the email with the few license lines to copy in a file
> (that i created) name license.txt
> I created a new file and erased the existing LICENSE
>
> Thanks
> Marco Ganzetti
>
> Last login: Fri Dec 16 16:56:54 on ttys002
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
> Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
> Binds-MacBook-Pro:~ Marco$ export
> SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN
> Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
> --regheader elab --hemi lh --o
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
> srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>   Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target
> reference.
> Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 41923
> Writing to
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
> Dim: 116772 1 1
> Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay
> /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
> subject is elab
> hemiis lh
> surface is inflated
> surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /Users/Marco
> checking for nofix files in 'inflated'
> Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab)
> Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
> surfer: Reading header info from
> /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> Binds-MacBook-Pro:~ Marco$
>
> - - -
>
> *Marco Ganzetti, PhD*
>
> Movement Control & Neuroplasticity Research Group
> Tervuursevest 101, 3001 Leuven
>
> email: marco.ganze...@kuleuven.be 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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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.

[Freesurfer] License problem

2016-12-16 Thread Marco Ganzetti

Dear all,
I am trying to display a volumetric file to a surface using mri_vol2surf and 
then tksurfer.
Here is the error message I get.

I have obtained the email with the few license lines to copy in a file (that i 
created) name license.txt
I created a new file and erased the existing LICENSE

Thanks
Marco Ganzetti

Last login: Fri Dec 16 16:56:54 on ttys002
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
Binds-MacBook-Pro:~ Marco$ export 
SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN
Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src 
/Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii  --regheader 
elab --hemi lh --o 
/Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target 
reference.
Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 41923
Writing to 
/Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
Dim: 116772 1 1
Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay 
/Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
subject is elab
hemiis lh
surface is inflated
surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/Marco
checking for nofix files in 'inflated'
Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab)
Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
surfer: Reading header info from 
/Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
--
ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--
Binds-MacBook-Pro:~ Marco$

- - -

Marco Ganzetti, PhD

Movement Control & Neuroplasticity Research Group
Tervuursevest 101, 3001 Leuven

email: marco.ganze...@kuleuven.be

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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] License problem

2015-06-09 Thread Eric Achten


Dear FS,
I received my license e-mail for the upteenth time and converted the  
mail to license.txt in the $FREESURFER_HOME directory, but I stll get  
an error message:


mri_convert  
/home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri/rawavg.mgz  
/home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri/orig.mgz --conform

--
ERROR: Invalid FreeSurfer license key found in license file  
/usr/local/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.


FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Kernel info: Linux 3.16.7-21-desktop x86_64, OpenSuse 13,2

My license e-mail:
Here is your FreeSurfer license.  Place the four lines between the
CUT HERE markers in a file named license.txt in the directory pointed to
by the $FREESURFER_HOME environment variable (see the FreeSurfer  
documentation).


#---CUT HERE---
rik.ach...@ugent.be
6890
 *CdJfYHGQmvsk
 FS2s/1aGOIEXo
#---CUT HERE---

The information you submitted was:

title=MD


My license.txt in attachment.
Thank you for helping,
Best wishes,
Rik


rik.ach...@ugent.be
6890
 *CdJfYHGQmvsk
 FS2s/1aGOIEXo

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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.

Re: [Freesurfer] License problem

2015-06-09 Thread Z K

Hello,

Please refrain from sending the contents of the license file in the open 
to the freesurfer list.

Unfortunately this is a known issue for all Opensuse platforms versions 
greater than 12.1 and there are two potential solutions. The first is to 
copy /lib64/libcrypt-2.14.1.so from an Opensuse 12.1 installation to 
$FREESURFER_HOME/lib. Then make a symbolic link to it. Or 2) just 
download and install the dev version.

-Zeke

On 06/09/2015 12:14 PM, Eric Achten wrote:
 Dear FS,
 I received my license e-mail for the upteenth time and converted the
 mail to license.txt in the $FREESURFER_HOME directory, but I stll get an
 error message:

 mri_convert /home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri/rawavg.mgz
 /home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri/orig.mgz --conform
 --
 ERROR: Invalid FreeSurfer license key found in license file
 /usr/local/freesurfer/license.txt
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.


 FREESURFER_HOME: /usr/local/freesurfer

 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

 Kernel info: Linux 3.16.7-21-desktop x86_64, OpenSuse 13,2

 My license e-mail:
 Here is your FreeSurfer license.  Place the four lines between the
 CUT HERE markers in a file named license.txt in the directory pointed to
 by the $FREESURFER_HOME environment variable (see the FreeSurfer
 documentation).

 #---CUT HERE---
 rik.ach...@ugent.be
 6890
   *CdJfYHGQmvsk
   FS2s/1aGOIEXo
 #---CUT HERE---

 The information you submitted was:

 title=MD
 

 My license.txt in attachment.
 Thank you for helping,
 Best wishes,
 Rik




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

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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.

Re: [Freesurfer] License problem

2013-06-13 Thread Claus Svarer

Thanks again for the answers, I have now got it working. It was my 
fault, I thought the name should be libcrypt.so and not as I found out 
it should be libcrypt.so.1.


So the solution for OpenSUSE 12.3 (64 bit) is to copy e.g. 
/lib64/libcrypt-2.14.1.so from an OpenSUSE 12.1 installation to 
freesurfer_home/lib. and then make a symbolic link to that, like ln 
-s libcrypt-2.14.1.so libcrypt.so.1 (also in freesurfer_home/lib). 
Actually the LD_LIBRARY_PATH already included this directory (even two 
times) while I have the command source 
$FREESURFER_HOME/SetUpFreeSurfer.sh in the .profile (we are using bash 
shell).


Thanks for the help

Claus




On 12-06-2013 19:13, Z K wrote:

Yes, I agree. Setting/appending to the LD_LIBRARY_PATH should be the
last thing you do just before issuing a freesurfer command. At the
moment Im unsure of the details regarding various Freesurfer scripts,
and their ability to retain environment variables, but I would guess
that information is preserved since knowledge FREESURFER_HOME and
SUBJECTS_DIR is so often required.

If the /etc/csh.cshrc.local works than that is a good method as well.

We will be looking into this Opensuse 12.3 libcrypt
incompatibility, but shy of a new release of freesurfer (which is very
unlikely) the solution will almost certainly involve using the older
version of libcrypt and setting the LD_LIBRARY_PATH.

-Zeke

On 06/12/2013 01:01 PM, Nick Jones wrote:

Hi Claus,

I don't know what to say, it worked for me.

Make sure the permissions on the library file are ok, and confirm that
the LD_LIBRARY_PATH path is set properly before launching the freesurfer
command (the system should check that first).  I'm not sure if when
launching certain commands, freesurfer creates new shells that don't
have the variable set properly, which breaks it.  I set mine at shell
invocation using /etc/csh.cshrc.local and so that may make the
difference, but as you say, it is risky to override the system libcrypt.so

Thanks

Nick


On 06/12/2013 02:53 AM, Claus Svarer wrote:

Thank you for all the answers, I am sure it has something to do with
this crypt shared library as when I replace the /lib64/libcrypt.so
with the OpenSuse 12.1 version tkmedit can start. This is though a bit
risky as there may be other routines including the operating system,
that uses the new updated library.

Unfortunately, the proposed solution about copying the libcrypt.so to
freesurfer/lib and then add that path to the $LD_LIBRARY_PATH does not
work. Any other idea about how to make the old libcrypt.so accessible
to freesurfer routines?

Thanks
Claus


On 11-06-2013 20:00, Z K wrote:

Thank you Nick for informing the list of this workaround.

-Zeke

On 06/11/2013 01:48 PM, Nick Jones wrote:

Regarding any license issue under Opensuse 12.3 and the libcrypt
incompatibility.

So grab a libcrypt from an older opensuse (one where freesurfer was
working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better
candidate if it works).  Place it somewhere ($FREESURFER_HOME/lib is a
good candidate), then add the location to the LD_LIBRARY_PATH
environment variable so that freesurfer finds the old libcrypt.

There is another workaround but you must contact Nick Schmansky, I
don't
remember the details.

Thanks

Nick




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[Freesurfer] License problem

2013-06-11 Thread Claus Svarer


Hi

We have just updated one of our Linux servers from OpenSuse v. 12.1 to 
12.3. After the update we get the following license error message  for 
some of the freesurfer commands:


csvarer@hevesy:/usr/local/nru/freesurfer tkmedit -help
--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/nru/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--


W have another server still running the older OpenSuse version and there 
it works without any problems. There hasn't been done any changes to the 
freesurfer installation directory and it is the same shared NFS mounted 
directory at both servers. Please help us finding out how to correct 
this problem so we can use Freesurfer again.


Thanks for the help
Claus Svarer
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] License problem

2013-06-11 Thread Douglas Greve



Hi Claus, I have never seen this before. Maybe Zeke has an idea?
doug




On 6/11/13 5:02 AM, Claus Svarer wrote:

Hi

We have just updated one of our Linux servers from OpenSuse v. 12.1 to 
12.3. After the update we get the following license error message  for 
some of the freesurfer commands:


csvarer@hevesy:/usr/local/nru/freesurfer tkmedit -help
-- 

ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/nru/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
-- 




W have another server still running the older OpenSuse version and 
there it works without any problems. There hasn't been done any 
changes to the freesurfer installation directory and it is the same 
shared NFS mounted directory at both servers. Please help us finding 
out how to correct this problem so we can use Freesurfer again.


Thanks for the help
Claus Svarer


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Re: [Freesurfer] License problem

2013-06-11 Thread Claus Svarer


Hi Doug

After having sent the message to the mailing list this morning I found 
another mail sent to the mailing list a month ago about same problem:


http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28264.html

I have tried to follow the thread but can't see that a solution was 
described. I therefor tried to email Nicola Toschi directly, but he has 
not answered yet. Let us see if he has found a solution for the problem.


Kind regards
Claus

On 11-06-2013 16:46, Douglas Greve wrote:


Hi Claus, I have never seen this before. Maybe Zeke has an idea?
doug




On 6/11/13 5:02 AM, Claus Svarer wrote:

Hi

We have just updated one of our Linux servers from OpenSuse v. 12.1 
to 12.3. After the update we get the following license error message  
for some of the freesurfer commands:


csvarer@hevesy:/usr/local/nru/freesurfer tkmedit -help
-- 

ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/nru/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
-- 




W have another server still running the older OpenSuse version and 
there it works without any problems. There hasn't been done any 
changes to the freesurfer installation directory and it is the same 
shared NFS mounted directory at both servers. Please help us finding 
out how to correct this problem so we can use Freesurfer again.


Thanks for the help
Claus Svarer


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

Re: [Freesurfer] License problem

2013-06-11 Thread Nick Jones

Regarding any license issue under Opensuse 12.3 and the libcrypt 
incompatibility.

So grab a libcrypt from an older opensuse (one where freesurfer was working, 
for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it 
works).  Place it somewhere ($FREESURFER_HOME/lib is a good candidate), then 
add the location to the LD_LIBRARY_PATH environment variable so that freesurfer 
finds the old libcrypt.

There is another workaround but you must contact Nick Schmansky, I don't 
remember the details.

Thanks

Nick
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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
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Re: [Freesurfer] License problem

2013-06-11 Thread Z K

Thank you Nick for informing the list of this workaround.

-Zeke

On 06/11/2013 01:48 PM, Nick Jones wrote:
 Regarding any license issue under Opensuse 12.3 and the libcrypt
 incompatibility.

 So grab a libcrypt from an older opensuse (one where freesurfer was
 working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better
 candidate if it works).  Place it somewhere ($FREESURFER_HOME/lib is a
 good candidate), then add the location to the LD_LIBRARY_PATH
 environment variable so that freesurfer finds the old libcrypt.

 There is another workaround but you must contact Nick Schmansky, I don't
 remember the details.

 Thanks

 Nick


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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] license problem - please help

2009-12-28 Thread tracy butler

I've pasted the error message (and all the preceding command lines) below.
I'm using the latest version of ubuntu in virtualbox. I made the .license
file w/ pico, and it looks fine to me, but it's just not working.

Thanks for any help!

tracy

 

tr...@covet:~$ tcsh

covet:~ setenv FREESURFER_HOME /usr/local/freesurfer

covet:~ source $FREESURFER_HOME/SetUpFreeSurfer.csh

 freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /usr/local/freesurfer

FSFAST_HOME   /usr/local/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii

SUBJECTS_DIR  /usr/local/freesurfer/subjects

MNI_DIR   /usr/local/freesurfer/mni

covet:~ more /usr/local/freesurfer/.license 

tab2...@med.cornell.edu

8222

 *CTAeXNprjJ6

covet:~ tkmedit bert orig.mgz

OpenGL Warning: Failed to connect to host. Make sure 3D acceleration is
enabled for this VM.

--

ERROR: Invalid FreeSurfer license key found in license file
/usr/local/freesurfer/.license

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to 

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

--

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Re: [Freesurfer] license problem - please help

2009-12-28 Thread Bruce Fischl

Hi Tracy,

it looks like there is some line before the email address, and before the 
other 2 lines as well. If you cat the .license they should show up as three 
consecutive lines with no blank lines between them. Try looking at it in 
emacs.

cheers
Bruce


On Mon, 28 Dec 2009, 
tracy butler wrote:

 I've pasted the error message (and all the preceding command lines) below.
 I'm using the latest version of ubuntu in virtualbox. I made the .license
 file w/ pico, and it looks fine to me, but it's just not working.

 Thanks for any help!

 tracy



 tr...@covet:~$ tcsh

 covet:~ setenv FREESURFER_HOME /usr/local/freesurfer

 covet:~ source $FREESURFER_HOME/SetUpFreeSurfer.csh

  freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 

 Setting up environment for FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME   /usr/local/freesurfer

 FSFAST_HOME   /usr/local/freesurfer/fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR  /usr/local/freesurfer/subjects

 MNI_DIR   /usr/local/freesurfer/mni

 covet:~ more /usr/local/freesurfer/.license

 tab2...@med.cornell.edu

 8222

 *CTAeXNprjJ6

 covet:~ tkmedit bert orig.mgz

 OpenGL Warning: Failed to connect to host. Make sure 3D acceleration is
 enabled for this VM.

 --

 ERROR: Invalid FreeSurfer license key found in license file
 /usr/local/freesurfer/.license

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

 --


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Re: [Freesurfer] License problem

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[Freesurfer] License problem

[Freesurfer] License problem

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Re: [Freesurfer] License problem

[Freesurfer] License problem

Re: [Freesurfer] License problem

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Re: [Freesurfer] License problem

[Freesurfer] license problem - please help

Re: [Freesurfer] license problem - please help

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