Re: [Freesurfer] Freesurfer installation issue

[fsbuild]

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 Try using apt to do the install, and you could also preface the package 
name with its absolute path, /path/to/package
$ sudo apt install /path/to/package/freesurfer_7.2.0_amd64.deb
- R.
On Jul 15, 2023, at 05:02, Ramesh Babu  
wrote:External Email - Use 
CautionDear Expert,I am trying 
to install Freesurfer-7.2 .deb package. I had this package earlier, and 
after formatting my system now, I am trying to install Freesurfer again. But I 
am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a 
Debian format archivedpkg: error processing archive freesurfer_7.2.0_amd64.deb 
(--install): dpkg-deb --control subprocess returned error exit status 
2Errors were encountered while 
processing: freesurfer_7.2.0_amd64.debKindly request you to provide a 
solution to solve this issue.Thanks in 
advanceRamesh___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Freesurfer installation issue

[Ramesh Babu]

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Dear Expert,

I am trying to install Freesurfer-7.2 .deb package. I had this package
earlier, and after formatting my system now, I am trying to install
Freesurfer again. But I am facing the following issues.

'freesurfer_7.2.0_amd64.deb' is not a Debian format archive
dpkg: error processing archive freesurfer_7.2.0_amd64.deb (--install):
 dpkg-deb --control subprocess returned error exit status 2
Errors were encountered while processing:
 freesurfer_7.2.0_amd64.deb

Kindly request you to provide a solution to solve this issue.

Thanks in advance
Ramesh
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[Freesurfer] Freesurfer installation help

[Michael Mc Laughlin]

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You seriously need to improve the installation help for non-linux experts.

I spent six hours trying to upgrade from 7.3.2 to 7.4.1. The first 40
minutes was going through your help pages and reading very carefully
starting here:

https://secure-web.cisco.com/19ID4blh6dH7zLY1eBU3QOvif6gsUtz6XQjFV1RthoGhJDP4g3JcI2NFqZ3XIy03oN2w-27smG46dmvFHKL92qHZEwxnfZfJqTpI97n8jEelmHGJowDLEUlv1wevw-VIpbnXMZFYAi6Buv8okk0I_-cM7r5ytP4xNvyoq2JnTEuQRUWddnFtyrCU3fBHVXVIlUTNWpDjIFDUa9ccJAE5CO46qkqj85-AEf33uYFOzJuVmst58hqD7NNTnOBVWiS_Hqgnzo63U26tLTRdh_WkngjPImt4twYpXEN345uIahxNYwHYz8x3w0E8VwMKRmLZo/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FDownloadAndInstall
and here:
https://secure-web.cisco.com/1G2hfa6Pr6IRUiy_FTikis58foj-czVVon8c5s59_Asqy8yqRmbB8nZjNNIAZXjiswxhWPB7uOdOFTeo_aw9LX9L1Y2T-LreT942RuNYgDxmMwPisngiDtA61BzPbb3kgcF-TnmdhJhGWV-ElY5szkKu7oImmCLItjXGpU4i2-eH7le0T88vF_S4mGyV-VpPmTsX9BcGmEuc-EXRwpd5cqBBi9YuQ6lxePKp070tWCXp2uDxr_SfGyokqustqEvtQGR4GtPEOAOVaTCONl711I0V4YFxMRcE4NeMOGs0vkZSOiFI04VMw9We_oxvEtY4f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
and many other linked pages

Only to find that there are not actually any instructions on what to do.

All you needed to say was:

*Find out what version of Linux you have with the command:*
cat /etc/os-release

*Download the appropriate file e.g. for Ubuntu 22 use the Deb installation
file*
freesurfer_ubuntu22-7.4.1_amd64.deb

*Then, for Ubuntu, install with the command*
sudo dpkg --install 

That would have saved me 6 hours!

I don't know linux so I don't know these basic commands.

A big problem for me was that I didn't know what version of Ubuntu I had
but I didn't know that I didn't know that and none of the installation
tools I tried told me, they just gave me unintelligible errors.

I think that because you are all linux fluent you have blind spots about
some of this basic stuff.

Michael McLaughlin,
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[Freesurfer] Freesurfer installation

[Stefan Rampp]

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Dear Freesurfer developers,

For the installation of Freesurfer, I'd need a pass code to extract the zip
file.

Best regards
Stefan
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Re: [Freesurfer] FreeSurfer installation in a Code Ocean Capsule

[fsbuild]

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Hello Chiara,
It reads like Code Ocean wants to be a solution for someone to host all their 
research files for published articles, scripts, applications and binaries to 
run - in 1 place.  But it’s not clear to me applications/scripts/binaries 
can be run from there in real-time.  It looks more like another form of 
source control, e.g., GitHub, to enable sharing and managing of files 
(including disaster recovery). 
The text at the bottom of this 
page, https://secure-web.cisco.com/1aH9sOdWmoRBiry1WokL4RYzdttBbVqc-sCSp1N3OC-uGLT2qBkRJd6vqH3_fkvCX_A6IeReQhXDV2cEVEr8ToFCntucsRr9gnDHMjk384H_-Q_EtelHBLQvoNGEV0WPb5rRrd9IqfgBgJyLZi0pH3R-ncw7k8M7mOXyOL8657_-_pCi1IEhefF7NrFSR_d93m2l4rKYKtFtU6dXKc0MtGYoCugqOX-pSzYoz24rLAFyzERSTWodnQt-htayc5ONZeb0pfKf4McsLEspxf_0qsMwt3eAH97IzcXfdIjz1VHQl2qNzsKsfhY6cyPIxReOYVmTz7XDrqf0p9Lrte0wnQg/https%3A%2F%2Fcodeocean.com%2Fproduct%2F,
 indicates they use Amazon AWS servers.  So maybe a code capsule would 
connect with and run software via an AWS server image with the needed software 
installed.  That server would in turn need to run a flavor of linux that 
would allow installing one of the freesurfer distribution packages 
from https://secure-web.cisco.com/17phn5CctlPx0-cSxitH_2EOSCGyEjytacc8qy9k2RLxkApD7ge8Mfi1dpgW1O7dZgG-LaWUrc0zEs9aYC2Zz8jxtqJ6ZTqzlIMnhTUtk0omBjE0fW25UJRiG_PwLSjRu4nmH9X-7mIdnQ5j4CO_nmimb9ihj58KPkUrDS5uWrl7rQ4-5EVj7uxWvz1zOA2oIq_L1g3Zo1IeMpbu4WSuxVvzTONuQuAhstcnoVUDC7wPhyL8dLY8lt0YqPlrvKUzAH9NugLd919ikUCmtw7LEpw46to5_b19MSdho4fgFoMwKGe62RRZlOUFgCjootxbF63hdmd6-9gajYEqeBHWZMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
For scientific clusters, you usually file a ticket to request installation of a 
software package not already available to run on the cluster.  I would ask 
Code Ocean tech support how a code capsule currently runs python scripts and/or 
linux binaries in real-time from a users account.  If that already works 
to run python scripts or some programs installed on linux servers, then you 
could ask tech support how 3rd party software packages (like freesurfer) could 
be managed and installed to run from a users account.
- R.

On Feb 24, 2023, at 03:50, Chiara Marzi - UniFI  
wrote:External Email - Use 
CautionDear Freesurfer,
I am trying to use some FreeSurfer tools inside a Code Ocean capsule 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
be https://secure-web.cisco.com/1-WWfxxHb5KgsxJyNmbX2M5iZmuUeIU8z2QsbWvYbriKD4AiU_FiRgf_eKbJMPcvo_KHOjz9fkbjdakm3l1Owhy7wMf57UYVKMTewVwC5tACzxW5VnE92lZnHtBGaRkXJqAfzC0s99373tnftyarXoU6SIWCnq_ffvXgBSfdqXMrYtZARIsfWPz6W5Cp2PQRYOhokfl0BwjpaPref7xCvH980up8AIHjgQLTfZa7Y5ZL9K-SMJasb64jB5ss9i_dN-_pSHNm0CIjI6TveSPzGK7mQBJvfU5bk73lnEm7OJ4I9ICHDRrJ6oURs_oma-WhU9Z0pTx36r6pE731zrTGb_g/https%3A%2F%2Fcodeocean.com%2F), a
 cloud-based computational reproducibility platform that provides researchers 
and developers an easy way to share, discover, and run code published in 
academic journals and conferences. Specifically, I set up my capsule 
environment including a Python package (freely available at Github: XXX) that 
requires FreeSurfer for full functionality. Is it possible to install 
FreeSurfer on such a platform? Do you have any suggestions?Thanks!Have a nice 
day,Chiara___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] FreeSurfer installation in a Code Ocean Capsule

[Chiara Marzi - UniFI]

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Dear Freesurfer,

I am trying to use some FreeSurfer tools inside a Code Ocean capsule 
(https://secure-web.cisco.com/1F1n6n0E7KQZBogoJ-y7cciJe_z3d-WxxhEPHp2zwkasImEBZvKePlK6P71av7i50AM4Z0TPRLdriPQ7fWxL-OnFfVOJBHQItgkdxdjByqeRfMyJTCMrcEaYvsJALn5lt0BoJz9mhOnZov_LnVy8BA9UxVAXV9lPIp95DeliRnEb7EglpOU15Cr01bkzW-Ujv_8-zio2c4flgN5rCGeA5OvdySKaFfr5FqLTVxhbh2XdyazQPvbl659YegRcnM3r5hRW7YC3DI5LZ8SglrZ_BCNJxxDeSphOLIyb5Gp3p9dwI4HC8JjcVZ50qJtXwEr5WYGcmnTNER5j7w-2CdJB9gA/https%3A%2F%2Fcodeocean.com%2F),
 a cloud-based computational reproducibility platform that provides researchers 
and developers an easy way to share, discover, and run code published in 
academic journals and conferences. 

Specifically, I set up my capsule environment including a Python package 
(freely available at Github: XXX) that requires FreeSurfer for full 
functionality. Is it possible to install FreeSurfer on such a platform? Do you 
have any suggestions?

Thanks!

Have a nice day,
Chiara___
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[Freesurfer] freesurfer installation pass code request

[심정민]

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Hi, I have downloaded the Freesurfer Virtualbox VM images.



Would you please send me the pass code?



Sincerely,
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Re: [Freesurfer] Freesurfer installation error?

[Banik, Rana]

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This installation worked accordingly:
https://secure-web.cisco.com/1MJ_TJWUMjY6Ctscf9lAD3FAyQ0T6kPXgTypmYhYSIpPMR9mpI5adFL530QZxv9glpK-VU_Vt31XgVIwaTHqrEYMBy7IF_aBFuxwAnHi-kFJRosFDhkX40mk7SzC_U0nw_PuPSk1GQ9UHadl_bq-QAlQkuYK06-rseLn5oIg7nqgI7ZiPUhYbCKR6NcLopCG_GolXi5TMROtcL1uIRwfM_Xf8MoedKCPABmU6w4gTlmEVGktuTaab3aOHuiWvGuE5FU_zcChO2wpCzEctGsZ-BA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_linux%23%3A%7E%3Atext%3D%2524%2520cd%2520%2524HOME%250A%2524%2520pwd%250A%2Fhome%2Ftester%250A%2524%2520sudo%2Cfreeview%250A%2Fusr%2Flocal%2Ffreesurfer%2Fbin%2Ffreeview


banikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurfer
banikr2@banikr:~$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects
banikr2@banikr:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
banikr2@banikr:~$ which freeview
/usr/local/freesurfer/bin/freeview

Are there any other checks to ensure the correct installation?

Rana Banik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Banik, Rana 

Sent: Sunday, September 26, 2021 4:08 AM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Freesurfer installation error?


External Email - Use Caution

Hello,
Please see the following installation I attempted.

banikr2@banikr:~$ which yum
I already had a previous faulty freesurfer installed.
banikr2@banikr:~$ ls -l -h

drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  
freesurfer-linux-centos6_x86_64-7.1.1.tar.gz


For some reason, the freesurfer directory had only 4Kb size.


banikr2@banikr:~$ rm -rf freesurfer
banikr2@banikr:~$ ls -l -h


-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  
freesurfer-linux-centos6_x86_64-7.1.1.tar.gz



banikr2@banikr:~$ cd $HOME
banikr2@banikr:~$ sum freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
55852 4560006


banikr2@banikr:~$ tar zxpf freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
banikr2@banikr:~$ ls -l -h


drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  
freesurfer-linux-centos6_x86_64-7.1.1.tar.gz



banikr2@banikr:~$ ls freesurfer
ASegStatsLUT.txt  DefectLUT.txt  FreeSurferColorLUT.txt  fsfast  python 
  SetUpFreeSurfer.sh subjects  WMParcStatsLUT.txt
average   diffusion  FreeSurferEnv.csh   lib 
SegmentNoLUT.txt Simple_surface_labels2009.txt  tkmeditParcColorsCMA
bin   docs   FreeSurferEnv.shmatlab  sessions   
  sources.cshtktools
build-stamp.txt   etcfsafd   mni 
SetUpFreeSurfer.csh  sources.sh trctrain
banikr2@banikr:~$ export FREESURFER_HOME=$HOME/freesurfer
banikr2@banikr:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /usr/local/freesurfer/fsfast does not exist
FREESURFER_HOME   /home/banikr2/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/banikr2/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist.
FSL_DIR   /usr/local/fsl



banikr2@banikr:~$ ls -l -h

drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer -rwxrwxrwx  1 
banikr2 banikr2  4.4G Sep 24 13:17  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

The same error persists.

Rana Banik


From: fsbuild 
Sent: Saturday, September 25, 2021 8:23 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Banik, Rana 
Subject: Re: [Freesurfer] Freesurfer installation error?

It looks like you want to install and run the 7.1.1 release on CentOS6.

The fsfast and mni subdirectories are in the distribution, so I am not sure why 
you are getting that output.  I suggest trying to do a clean install from 
scratch.  There are a couple of ways to do that, i.e., clean install under 
/usr/local  and-or  clean install under your home ($HOME) directory.  I will 
list instructions for both.

If you already installed under /usr/local, then you should have sudo/admin 
privileges to write files there.   A simple way to check that is to try and run 
a harmless command with sudo, e.g.,

$ sudo date
[sudo] password for :   <—— enter your password

If your password is accepted then the date command will run and p

Re: [Freesurfer] Freesurfer installation error?

[Banik, Rana]

External Email - Use Caution

Hello,
Please see the following installation I attempted.

banikr2@banikr:~$ which yum
I already had a previous faulty freesurfer installed.
banikr2@banikr:~$ ls -l -h

drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  
freesurfer-linux-centos6_x86_64-7.1.1.tar.gz


For some reason, the freesurfer directory had only 4Kb size.


banikr2@banikr:~$ rm -rf freesurfer
banikr2@banikr:~$ ls -l -h


-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  
freesurfer-linux-centos6_x86_64-7.1.1.tar.gz



banikr2@banikr:~$ cd $HOME
banikr2@banikr:~$ sum freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
55852 4560006


banikr2@banikr:~$ tar zxpf freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
banikr2@banikr:~$ ls -l -h


drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  
freesurfer-linux-centos6_x86_64-7.1.1.tar.gz



banikr2@banikr:~$ ls freesurfer
ASegStatsLUT.txt  DefectLUT.txt  FreeSurferColorLUT.txt  fsfast  python 
  SetUpFreeSurfer.sh subjects  WMParcStatsLUT.txt
average   diffusion  FreeSurferEnv.csh   lib 
SegmentNoLUT.txt Simple_surface_labels2009.txt  tkmeditParcColorsCMA
bin   docs   FreeSurferEnv.shmatlab  sessions   
  sources.cshtktools
build-stamp.txt   etcfsafd   mni 
SetUpFreeSurfer.csh  sources.sh trctrain
banikr2@banikr:~$ export FREESURFER_HOME=$HOME/freesurfer
banikr2@banikr:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /usr/local/freesurfer/fsfast does not exist
FREESURFER_HOME   /home/banikr2/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/banikr2/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist.
FSL_DIR   /usr/local/fsl



banikr2@banikr:~$ ls -l -h

drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer -rwxrwxrwx  1 
banikr2 banikr2  4.4G Sep 24 13:17  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

The same error persists.


Rana Banik


From: fsbuild 
Sent: Saturday, September 25, 2021 8:23 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Banik, Rana 
Subject: Re: [Freesurfer] Freesurfer installation error?

It looks like you want to install and run the 7.1.1 release on CentOS6.

The fsfast and mni subdirectories are in the distribution, so I am not sure why 
you are getting that output.  I suggest trying to do a clean install from 
scratch.  There are a couple of ways to do that, i.e., clean install under 
/usr/local  and-or  clean install under your home ($HOME) directory.  I will 
list instructions for both.

If you already installed under /usr/local, then you should have sudo/admin 
privileges to write files there.   A simple way to check that is to try and run 
a harmless command with sudo, e.g.,

$ sudo date
[sudo] password for :   <—— enter your password

If your password is accepted then the date command will run and print out the 
date.  If not,  it will ask you to enter a password again.  If your password 
does not work then it means you do not have sudo privileges and you won't be 
able to run the installer.  In that case, hit Ctrl-C to get out of the password 
prompt and go to INSTALL IN HOME DIRECTORY below.  You should not need any 
special privileges to write or delete files on your home directory.

CLEAN INSTALL IN /USR/LOCAL

Only try this if sudo/admin privileges worked above for the command “sudo date”.

First make sure you have the “yum” command installed,
$ which yum
/usr/bin/yum

If you don’t have the yum package manager command installed, then stop and go 
to the instructions for  INSTALL IN HOME DIRECTORY.

If you do have the yum command, then make sure you can download the CentOS6 
installer.  You can download this directly into your home directory from the 
terminal,

$ cd $HOME

… get the 7.1.1 installer for CentOS6 … if wget does not work or you don’t have 
that command you can use that link in your browser to download it ...

$ wget  
https://secure-web.cisco.com/1OcnxOZFDeUNyl0BK0ywbIoFU3iOV-hHXijiYm9AQcAXNY8ozu40qyd3tPQ6s_Q57EOHb8TcLxGr71qzKoQbTh7SDlKsVDDkCdOznBMDj49b4nxWKFYeOoBS1A1C0UFsvOW8mACmu9qZh_Pet8QB1BrtpdhH21DAoD3q9lVIhuC8StPLaGJqnj-j6pySt-FcyXPPmriivNPLQU_3vwQq_5Uk2o4YlzRAlfymlCu4YUrjZzEQzSyGuKPQK_BhQuSxmMEZ7n-D7GzlZzW2devASLA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-CentOS6-7.1.1-1.x86_64.rpm<https://secure

Re: [Freesurfer] Freesurfer installation error?

[fsbuild]

External Email - Use Caution

It looks like you want to install and run the 7.1.1 release on CentOS6.
The fsfast and mni subdirectories are in the distribution, so I am not sure why 
you are getting that output.  I suggest trying to do a clean install from 
scratch.  There are a couple of ways to do that, i.e., clean install under 
/usr/local  and-or  clean install under your home ($HOME) directory. 
 I will list instructions for both.

If you already installed under /usr/local, then you should have sudo/admin 
privileges to write files there.   A simple way to check that is to try 
and run a harmless command with sudo, e.g.,
$ sudo date[sudo] password for :       <—— 
enter your password
If your password is accepted then the date command will run and print out the 
date.  If not,  it will ask you to enter a password again.  If 
your password does not work then it means you do not have sudo privileges and 
you won't be able to run the installer.  In that case, hit Ctrl-C to get 
out of the password prompt and go to INSTALL IN HOME DIRECTORY below.  You 
should not need any special privileges to write or delete files on your home 
directory.
CLEAN INSTALL IN /USR/LOCAL
Only try this if sudo/admin privileges worked above for the command “sudo date”.
First make sure you have the “yum” command installed,$ which yum/usr/bin/yum
If you don’t have the yum package manager command installed, then stop and go 
to the instructions for  INSTALL IN HOME DIRECTORY.
If you do have the yum command, then make sure you can download the CentOS6 
installer.  You can download this directly into your home directory from 
the terminal,
$ cd $HOME
… get the 7.1.1 installer for CentOS6 … if wget does not work or you don’t have 
that command you can use that link in your browser to download it ...
$ wget 
 https://secure-web.cisco.com/1B_8WKZfHlV6TNLk-tm-JksrqbEl40VQhIwjbDLmV-ylwU7XH2EAqoO0Q7d0jXgZYHu0VPnch3AqmZKjSQ0Bmdebm4YLKAOoiZw0fR48S37iQnvyrf2KLOnQUwBsuIUSGrYnPw2U_Wj683TRLq66t6yEJulO5HYRowoqIwKAjgfBMEJzXntKwrgg8YAJ6LjGkScOtif3h6bAalhL6heDeKv7_-zsKJMqdQdWWP4ruGGoDgkL9qlD2oRte-HOYVidpbK6L36OK2J0pnVvwuBGFKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-CentOS6-7.1.1-1.x86_64.rpm
… wait for the download to finish via its progress bar and then check you have 
the complete installer file ...
$ sum  freesurfer-CentOS6-7.1.1-1.x86_64.rpm53407 3836829
If you did not get those exact numbers from the output of the checksum command, 
then re-try your download until you get that result.  If you can’t get the 
download to work then go to instruction for INSTALL IN HOME DIRECTORY.
If the download worked, then remove any existing freesurfer installation under 
/usr/local
$ cd /usr/local$ ls
If you do not see a freesurfer subdirectory then skip the next 2 commands 
(chmod and rm) and proceed to running the installer,
$ sudo chmod -R 777 freesurfer$ sudo rm -rf freesurfer
Now ls and make sure no freesurfer directory is there,
$ ls
Now try running the installer from your home directory,
$ cd $HOME$ sudo  yum  —nogpgcheck  localinstall   
freesurfer-CentOS6-7.1.1-1.x86_64.rpm
… answer y (for yes)  to any questions and wait for the install to finish …
Now do an ls of the new installation,
$ ls /usr/local/freesurfer/7.1.1-1
… and you should see both an fsfast and mni subdirectory there.
Try setting the environment again but with FREESURFER_HOME set to the new 
install path,$ export FREESURFER_HOME=/usr/local/freesurfer/7.1.1-1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh

CLEAN INSTALL IN HOME DIRECTORY

This should work no matter what is or is not installed under /usr/local.
Go to your home directory (always set as the value of the environment variable 
HOME)
$ cd $HOME
… get the 7.1.1 tar archive for CentOS6 …  if wget does not work or you 
don’t have that command you can use that link in your browser to download it ...
$ wget 
 https://secure-web.cisco.com/11zPV9NZ3Ex-1wASONnitG0xlqQgwcqw2vL1B1sywAZjAqytIaxxH3dJltyOPZMdcURt-onoPFGK-61rYdFlH39LCy8XGcP_QqK0RQt5n_T6pzBopyhoAr4Lof7I0WVP-JjBVv7HrKUXxGAgT7sFW7w_dK0TUCw6Y8PK7B1C3fC7_v2n38BIM9vsvz_wLV5kt5EBLQIAXxkOfqviOtQPr5szURoGI3FF5LlLJ7gQRT_7n2kOELAjU4wlWpk30C_kYnZbC47IZR8hsoKNNcslc4g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-linux-centos6_x86_64-7.1.1.tar.gz
… wait for the download to finish via its progress bar and then check you have 
the complete archive file ...
$ sum  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz55852 4560006
If you did not get those exact numbers from the output of the checksum command, 
then re-try your download until you get that result.
If the download worked, then remove any existing freesurfer installation 
$ ls
If you do not see a freesurfer subdirectory then skip the “rm” command
$ rm -rf freesurfer
Now unarchive the tar archive with,
$ tar zxpf freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
You should now have a ./freesufer directory under $HOME.  With ls 

[Freesurfer] Freesurfer installation error?

[Banik, Rana]

External Email - Use Caution

Installed freesurfer with the following errors.

banikr2@banikr:~/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /usr/local/freesurfer/fsfast does not exist
FREESURFER_HOME   /home/banikr2/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/banikr2/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist.
FSL_DIR   /usr/local/fsl

I can run freeview with the following:

banikr2@banikr:~/freesurfer$ freeview

Is the installation done correctly? Do the warnings compromise anything?

Rana Banik
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Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine

[fsbuild]

External Email - Use Caution

I should have said at the end for installation under $HOME to set,



$ export FREESURFER_HOME=$HOME/freesurfer





- R.


fsbuildMarch 3, 2020 at 15:39
  External Email - Use 
Caution
Hello Ben, 

For packages to install, see the following wiki page,
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements
Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would 
need sudo/root privileges, e.g.
$ cd /usr/local$ sudo tar 
zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz…... output 
deleted
- and you would end up with /usr/local/freesurfer and in turn do
$ export FREESURFER_HOME=/usr/local/freesurfer
But if you don’t have sudo privileges, e.g., it does not work to do$ sudo touch 
/usr/local/foo$ sudo rm /usr/local/foo
-
 then you may want to consider putting freesurfer under your $HOME 
directory or somewhere you have permission to write files w/o needing to
 use sudo, e.g.,
$ cd $HOME$ tar 
zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$ export 
FREESURFER_HOME=$HOME
- R.


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Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine

[fsbuild]

External Email - Use Caution

Hello Ben, 

For packages to install, see the following wiki page,
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements
Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would 
need sudo/root privileges, e.g.
$ cd /usr/local$ sudo tar 
zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz…... output 
deleted
- and you would end up with /usr/local/freesurfer and in turn do
$ export FREESURFER_HOME=/usr/local/freesurfer
But if you don’t have sudo privileges, e.g., it does not work to do$ sudo touch 
/usr/local/foo$ sudo rm /usr/local/foo
- then you may want to consider putting freesurfer under your $HOME directory 
or somewhere you have permission to write files w/o needing to use sudo, e.g.,
$ cd $HOME$ tar 
zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$ export 
FREESURFER_HOME=$HOME
- R.

On Mar 3, 2020, at 12:53, Benjamin Ineichen  
wrote:External Email - Use 
CautionDear Freesurfer 
experts,Even though this problem has been raised in the archives, I was not 
able to find a specific solution to my problem.I installed Freesurfer on a 
virtual machine which runs Ubuntu 18.04.4 (Host system: Windows 10). But it 
seems that Freesurfer is not installed properly. Upon running the installation 
test, I get the following errors:1.) command line: cp 
$FREESURFER_HOME/subjects/sample-001.mgz .Error: cp: cannot create regular file 
'./sample-001.mgz': Permission denied2.) command line: mri_convert 
sample-001.mgz sample-001.nii.gzError: mri_convert..bin sample-001.mgz 
sample-001.nii.gz$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 reuter Exp 
$reading from sample-001.mgz...mghRead(/usr/local/sample-001.mgz, -1): could 
not open file3.) command line: freeviewError: freeview.bin: error while loading 
shared libraries: libpng12.so.0: cannot open shared object file: No such file 
or directory.My permissions are: drwxrwsr-x for freesurfer.Any 
advice?Many thanks!/Ben-- Benjamin
 Victor Ineichen, MD PhDKarolinska InstitutetCenter for Molecular 
MedicineStockholm, swedenineic...@protonmail.ch+41 76 391 04 01Dr. med. et Dr. 
rer. nat. ETH Benjamin Victor IneichenKarolinska InstitutetCenter for Molecular 
MedicineStockholm, swedenineic...@protonmail.ch+41 76 391 04 
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[Freesurfer] Freesurfer installation on Ubuntu virtual machine

[Benjamin Ineichen]

External Email - Use Caution

Dear Freesurfer experts,

Even though this problem has been raised in the archives, I was not able to
find a specific solution to my problem.

I installed Freesurfer on a virtual machine which runs Ubuntu 18.04.4 (Host
system: Windows 10). But it seems that Freesurfer is not installed
properly. Upon running the installation test, I get the following errors:

1.) command line: cp $FREESURFER_HOME/subjects/sample-001.mgz .
Error: cp: cannot create regular file './sample-001.mgz': Permission denied

2.) command line: mri_convert sample-001.mgz sample-001.nii.gz
Error: mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 reuter Exp $
reading from sample-001.mgz...
mghRead(/usr/local/sample-001.mgz, -1): could not open file

3.) command line: freeview
Error: freeview.bin: error while loading shared libraries: libpng12.so.0:
cannot open shared object file: No such file or directory.

My permissions are: drwxrwsr-x for freesurfer.

Any advice?

Many thanks!

/Ben



-- 

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch
+41 76 391 04 01
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Re: [Freesurfer] FreeSurfer Installation

[Bruce Fischl]

try this page:

http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#FreeSurferDownloadandInstall

cheers
Bruce
On 
Mon, 22 Jan 2018, Caio Quini wrote:

> Hello
>
> I am trying to download FreeSurfer from freesurfer.net and I can't open the 
> download page.
> It keeps returning an error message.
> Is that a common error?
> Is there any other way to download the software?
> Thank you very much.
>
> Regards
>
> Caio Quini
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>
>
>
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[Freesurfer] FreeSurfer Installation

[Caio Quini]

Hello

I am trying to download FreeSurfer from freesurfer.net and I can't open the 
download page. 
It keeps returning an error message. 
Is that a common error? 
Is there any other way to download the software? 
Thank you very much. 

Regards

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

[Freesurfer] freesurfer installation through Virtual-box

[Anirban Sengupta]

Sir,
   I would like to install the Virtualbox version of freesurfer in
XUBuntu platform, version V5.3.0. However whenever I am clicking the link
for this, the download page which is opening is crashing. I have tried in
other systems. The Internet connection is also very good here. The page
that is opening is not a normal download file but a new page and it is
crashing after some time. Can you help me out or give some other link to
download it.
 I have FSL installed in my system.I installed FSL in Vmware with a
LInux CentOs platform. My question is, can I install freesurfer Linux
version in the same CentOs platform that I use for FSL. That would help me
bypass the previous problem which I am facing. Kindly reply.

-- 
Regards
Anirban Sengupta
Phd Scholar, CBME
IIT Delhi
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Re: [Freesurfer] Freesurfer installation problem

[Venkateswaran Rajagopalan]

Nick,

Thanks very much. I will do as per your suggestion. I am new to Linux and
Ubuntu.

If I am not bothering you too much. I read an article where they compared
the results
from Freesurfer's different versions and about using different OS and
concluded saying that
use the same version and do not upgrade while in the middle of the study.
My collaborators are using
Freesurfer 5.0 and I will be helping them in processing the data (sharing
the data processing and analysis)
so is it ok to use use 5.3.0 or 5.0 is recommended.

Thanks very much again
Venkat


On Wed, Jun 11, 2014 at 12:50 AM, Nick Schmansky, MGH <
ni...@nmr.mgh.harvard.edu> wrote:

> Venkat,
>
> Your system appears to be 32bit distribution, as indicated by 'i686' in
> your output string, but the freesurfer you installed is 64b, indicated
> by 'x86_64' in our filename.  So you will need the 32b dist:
>
> freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz
>
> Also, v5.0.0 is pretty old, I'd recommend v5.3.0.
>
> Nick
>
> On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote:
> > Dear All,
> >
> >
> > I looked into the archives extensively but could not find a solution
> > to my problem.
> >
> >
> > I am having Ubuntu " Linux administrator-HP-Pro-3330-MT
> > 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686
> > i686 i686 GNU/Linux".
> >
> >
> > I tried installing
> > freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get
> > the following error message
> >
> > mri_convert
> > /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file
> > not executable.
> >
> > tkmedit
> > /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary
> > file not executable.
> >
> >
> > I followed the instruction steps as given in freesurfer wiki. What am
> > I doing wrong here?. Is there a installation wiki page for giving
> > guidelines for ubuntu freesurfer installation.
> >
> >
> > Thanks, any help will be greatly appreciated as I am trying to install
> > freesurfer for the past 3 days without success.
> >
> >
> > Thanks
> >
> > Venkat
> >
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>
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Freesurfer installation problem

[Venkateswaran Rajagopalan]

Hi Bruce,

Thanks very much
What hardware platform are you running on?
Memory: 3.8 GiB
Processor Intel core i3-3220 cpu @3.30 GHz*4
Graphics Intel Ivybridge Desktop x86/MMX/SSE2
OS type 32-bit
Disk 103.1 GB

And can you run: ls -l  /usr/local/freesurfer/bin/mri_convert

I get the following when the run the above -rwxr-xr-x 1 root root 4015444
May 14  2013 /usr/local/freesurfer/bin/mri_convert

Thanks a lot

Venkat



On Tue, Jun 10, 2014 at 6:29 PM, Bruce Fischl 
wrote:

> Hi Venkat
>
> What hardware platform are you running on? And can you run:
>
> ls -l  /usr/local/freesurfer/bin/mri_convert
>
> cheers
> Bruce
>
> On Tue, 10 Jun 2014,
> Venkateswaran Rajagopalan wrote:
>
> > Dear All,
> >
> > I looked into the archives extensively but could not find a solution to
> my
> > problem.
> >
> > I am having Ubuntu " Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
> > #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux".
> >
> > I tried installing
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz.
> > But I get the following error message
> >
> > mri_convert
> > /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not
> > executable.
> >
> > tkmedit
> > /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file
> > not executable.
> >
> > I followed the instruction steps as given in freesurfer wiki. What am I
> > doing wrong here?. Is there a installation wiki page for giving
> guidelines
> > for ubuntu freesurfer installation.
> >
> > Thanks, any help will be greatly appreciated as I am trying to install
> > freesurfer for the past 3 days without success.
> >
> > Thanks
> > Venkat
> >
> >
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>
>
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> is
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Re: [Freesurfer] Freesurfer installation problem

[Nick Schmansky, MGH]

Venkat,

Your system appears to be 32bit distribution, as indicated by 'i686' in
your output string, but the freesurfer you installed is 64b, indicated
by 'x86_64' in our filename.  So you will need the 32b dist:

freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz

Also, v5.0.0 is pretty old, I'd recommend v5.3.0.

Nick

On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote:
> Dear All,
> 
> 
> I looked into the archives extensively but could not find a solution
> to my problem.
> 
> 
> I am having Ubuntu " Linux administrator-HP-Pro-3330-MT
> 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686
> i686 i686 GNU/Linux".
> 
> 
> I tried installing
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get
> the following error message 
> 
> mri_convert
> /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file
> not executable.
> 
> tkmedit
> /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary
> file not executable.
> 
> 
> I followed the instruction steps as given in freesurfer wiki. What am
> I doing wrong here?. Is there a installation wiki page for giving
> guidelines for ubuntu freesurfer installation.
> 
> 
> Thanks, any help will be greatly appreciated as I am trying to install
> freesurfer for the past 3 days without success.
> 
> 
> Thanks
> 
> Venkat
> 
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Re: [Freesurfer] Freesurfer installation problem

[Bruce Fischl]

Hi Venkat

What hardware platform are you running on? And can you run:

ls -l  /usr/local/freesurfer/bin/mri_convert

cheers
Bruce

On Tue, 10 Jun 2014, 
Venkateswaran Rajagopalan wrote:

> Dear All,
> 
> I looked into the archives extensively but could not find a solution to my
> problem.
> 
> I am having Ubuntu " Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
> #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux".
> 
> I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz.
> But I get the following error message
> 
> mri_convert
> /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not
> executable.
> 
> tkmedit
> /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file
> not executable.
> 
> I followed the instruction steps as given in freesurfer wiki. What am I
> doing wrong here?. Is there a installation wiki page for giving guidelines
> for ubuntu freesurfer installation.
> 
> Thanks, any help will be greatly appreciated as I am trying to install
> freesurfer for the past 3 days without success.
> 
> Thanks
> Venkat
> 
>
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[Freesurfer] Freesurfer installation problem

[Venkateswaran Rajagopalan]

Dear All,

I looked into the archives extensively but could not find a solution to my
problem.

I am having Ubuntu " Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
#46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux".

I tried installing
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the
following error message

mri_convert
/usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not
executable.

tkmedit
/usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file
not executable.

I followed the instruction steps as given in freesurfer wiki. What am I
doing wrong here?. Is there a installation wiki page for giving guidelines
for ubuntu freesurfer installation.

Thanks, any help will be greatly appreciated as I am trying to install
freesurfer for the past 3 days without success.

Thanks
Venkat
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Re: [Freesurfer] FreeSurfer installation

[Louis Nicholas Vinke]

Hi Neda,
Your terminal is probably setup to use the bash environment by default. 
If you type tcsh, then you'll be using C shell and that command should 
then work.  I see that this is not on the install page, but on the 
setup/config page there is a note about it.  There are also alternate 
commands to use for bash if you want on that page as well.

-Louis

On Wed, 22 Jan 2014, Neda Mohammadi wrote:


Hi dear Louis,
yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but 
when I write this command setenv FREESURFER_HOME
/usr/local/freesurfer I see this message:
bash: setenv: command not found

best,
Neda



On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke 
 wrote:
  Hi Neda,
  Have you read over the linux install directions in the link below?  You 
will need to register and get a license file.
   After that you should look over the setup and config instructions.

  https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall
  https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration

  -Louis

  On Wed, 22 Jan 2014, Neda Mohammadi wrote:

Hi dear all,
I want to use freesurfer for tractography by FSL.
I downloaded 
freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I
want to install it but I don't know how.

Please help me.
Thanks in advance,
Neda




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Re: [Freesurfer] FreeSurfer installation

[Neda Mohammadi]

Hi dear Louis,

yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but
when I write this command setenv FREESURFER_HOME /usr/local/freesurfer I
see this message:
bash: setenv: command not found

best,
Neda



On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke <
vi...@nmr.mgh.harvard.edu> wrote:

> Hi Neda,
> Have you read over the linux install directions in the link below?  You
> will need to register and get a license file.  After that you should look
> over the setup and config instructions.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall
> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
>
> -Louis
>
>
> On Wed, 22 Jan 2014, Neda Mohammadi wrote:
>
>  Hi dear all,
>> I want to use freesurfer for tractography by FSL.
>> I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>> and I
>> want to install it but I don't know how.
>>
>> Please help me.
>> Thanks in advance,
>> Neda
>>
>>
>>
>
> 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] FreeSurfer installation

[Louis Nicholas Vinke]

Hi Neda,
Have you read over the linux install directions in the link below?  You 
will need to register and get a license file.  After that you should look 
over the setup and config instructions.

https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration

-Louis

On Wed, 22 Jan 2014, Neda Mohammadi wrote:

> Hi dear all,
> I want to use freesurfer for tractography by FSL.
> I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I
> want to install it but I don't know how.
> 
> Please help me.
> Thanks in advance,
> Neda
> 
>
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[Freesurfer] FreeSurfer installation

[Neda Mohammadi]

Hi dear all,

I want to use freesurfer for tractography by FSL.
I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I
want to install it but I don't know how.

Please help me.
Thanks in advance,
Neda
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Re: [Freesurfer] Freesurfer installation error

[Octavian Lie]

solved, thank you,
Octavian


On Sat, Dec 21, 2013 at 11:55 AM, Octavian Lie wrote:

> Dear All,
>
> I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version
> (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf
> libraries missing in my distro, here is fs home directory:
>
> FREESURFER_HOME   /usr/local/fs5.3/freesurfer
> FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
> MNI_DIR   /usr/local/fs5.3/freesurfer/mni
>
> Testing using the commands on the testing page went OK, however, if I
> close the terminal, open another one, commands are not recognized, and I
> have to reset freesurfer home every time I open a terminal with
>
> setenv FREESURFER_HOME /freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> I thought this is a sudo issue, however if I use
>
> sudo setenv FREESURFER_HOME /usr/local/fs5.3/freesurfer, it tells me:
>
> sudo: setenv: command not found
>
>
> I mention I changed the default shell from bash to tcsh recently,
> Please advise,
>
> Octavian
>
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[Freesurfer] Freesurfer installation testing tksurfer error

[Octavian Lie]

Dear All,

I have recently upgraded freesurfer (dev version 12/19/2013 centos6,
86X64) on my ubuntu 12.04 box, I previously used v 5.1(centos 4).

I fixed all other issues that I posted about (libnetcdf
missing,.tcshrc editing), now all seems to go well, including testing,
except

when I load tksurfer bert rh pial, I see it well, and I can use
tksurfer tools well, as expected; however, if I want to close the
window
displaying surfaces (either before or after closing tksurfer tools
gui), I cannot; the only way to kill the process and exit tksurfer is
to close the terminal. Also, if I try to maximize the same window, I
get the following error:


surfer: Error sending tcl command MoveToolWindow 65 656:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed

I loaded other subjects previously processed with v5.1 version, and I
have the same issue. All other guis, including tkmedit, freeview and
qdec work well.

Please advise,

Octavian
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[Freesurfer] Freesurfer installation error

[Octavian Lie]

Dear All,

I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version
(12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf
libraries missing in my distro, here is fs home directory:

FREESURFER_HOME   /usr/local/fs5.3/freesurfer
FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
MNI_DIR   /usr/local/fs5.3/freesurfer/mni

Testing using the commands on the testing page went OK, however, if I close
the terminal, open another one, commands are not recognized, and I have to
reset freesurfer home every time I open a terminal with

setenv FREESURFER_HOME /freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

I thought this is a sudo issue, however if I use

sudo setenv FREESURFER_HOME /usr/local/fs5.3/freesurfer, it tells me:

sudo: setenv: command not found


I mention I changed the default shell from bash to tcsh recently,
Please advise,

Octavian
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Re: [Freesurfer] Freesurfer installation

[Z K]

Pablo,

That page "describes how to setup a personal laptop for usage in the 
Freesurfer course." It does not apply to a standard freesurfer 
installation.

Try opening a new terminal and typing "bash" before the "export" and 
"source" commands you give below.

-Zeke


On 07/17/2013 10:27 AM, pablo najt wrote:
> Dear Freesurfer experts,
>
>   I have a question regarding the installation/running of FreeSurfer.
>
> I have been trying to install freesurfer in a macbook pro (snow leopard)
> but no success.
>
> I followed the webpage from freesurfer (link below).
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup
>
>
> But after the installations when I open the terminal nothing happens.
>
>
> I also tried to launch freesurfer this way:
>
> export FREESURFER_HOME=/Applications/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> If I do this I get:
>
> command not found
>
> command not found
>
> command not found
>
>
> Any advice on how to finally set up the software would be great help.
>
> Thank you in anticipation.
>
> Pablo
>
>
>
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[Freesurfer] Freesurfer installation

[pablo najt]

Dear Freesurfer experts,
 I have a question regarding the installation/running of FreeSurfer.
I have been trying to install freesurfer in a macbook pro (snow leopard) but no 
success. 
I followed the webpage from freesurfer (link below). 


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup


But after the installations when I open the terminal nothing happens.


I also tried to launch freesurfer this way:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
If I do this I get:
command not found
command not found
command not found


Any advice on how to finally set up the software would be great help.
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[Freesurfer] freesurfer installation (fail)

[Daniël Höhle]

Hello there,

I''ve tried a couple installations of FreeSurfer as listed on the website. 
Though there seems to be a problem. Both linux tarballs seem to be designed for 
centos4, though that version is not supported anymore, so downloading is a 
pain, and accessing packages is out of the question.
The same thing I encountered for Xubuntu 9.04. Freesurfer works, though, but it 
is (vritually) impossible to get information from a winfows network, because 
nfs-common needs to be installed, and since Xubuntu 9.04 is not supported 
anymore (a bit over a year now), I cannot install the packages needed to access 
data.
Now I've downloaded Centos6 x86_32, I untarred the tarball, and I've set the 
environmental variables are listed.
Though if I try the command "tkmedit bert orig.mgz" I get 
"/usr/local/freesurfer/tktools/tkmedit.bin: Command not found". I don't know 
whether I should try and tweak the Centos6 version, or whether freesurfer will 
not run on this OS all together.
I got the impression that this project is still alive. Therefore I'd like to 
ask two questions:
1- can you, please, update the download section? FI virtual machine with Ubuntu 
10.04, and tarballs and information for Centos6?
2- can you help me with installing this on Centos6?

Kind regards,

Daniël Höhle

Scientific Programmer,
Alan Turing Institute Almere,
The Netherlands
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[Freesurfer] freesurfer installation (fail)

[Daniël Höhle]

Hello there,

I''ve tried a couple installations of FreeSurfer as listed on the website. 
Though there seems to be a problem. Both linux tarballs seem to be designed for 
centos4, though that version is not supported anymore, so downloading is a 
pain, and accessing packages is out of the question.
The same thing I encountered for Xubuntu 9.04. Freesurfer works, though, but it 
is (vritually) impossible to get information from a winfows network, because 
nfs-common needs to be installed, and since Xubuntu 9.04 is not supported 
anymore (a bit over a year now), I cannot install the packages needed to access 
data.
Now I've downloaded Centos6 x86_32, I untarred the tarball, and I've set the 
environmental variables are listed.
Though if I try the command "tkmedit bert orig.mgz" I get 
"/usr/local/freesurfer/tktools/tkmedit.bin: Command not found". I don't know 
whether I should try and tweak the Centos6 version, or whether freesurfer will 
not run on this OS all together.
I got the impression that this project is still alive. Therefore I'd like to 
ask two questions:
1- can you, please, update the download section? FI virtual machine with Ubuntu 
10.04, and tarballs and information for Centos6?
2- can you help me with installing this on Centos6?

Kind regards,

Daniël Höhle

Scientific Programmer,
Alan Turing Institute Almere,
The Netherlands
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Re: [Freesurfer] Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context

[Nick Schmansky]

this info might help:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11934.html

On Tue, 2010-12-07 at 13:58 -0500, dah...@nmr.mgh.harvard.edu wrote:
> Hi,
> 
> Would really appreciate help with this insallation problem!
> 
> I'm installing freesurfer on a new system, and at an initial test running
> "tkmedit bert.mgz" produces
> GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context.
> 
> I thought maybe updating the NVidia card would help, but when I go to
> their website and try to download NVidia Quadro NVS, there are only
> Windows options to select as OS.
> 
> This is a Dell Precision T7500 preinstalled with RHEL 5.4.
> 
> About a year ago I installed freesurfer on virtually identical hardware
> (the OS there was CentOS as a virtual machine under the Windows host), and
> did not run into such a problem
> 
> Can you help me figure out why it's running into this problem and how to
> fix it?
> 
> Thanks!
> Dahlia.
> 
> 
> 
> ___
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> 
> 

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[Freesurfer] Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context

[dahlia]

Hi,

Would really appreciate help with this insallation problem!

I'm installing freesurfer on a new system, and at an initial test running
"tkmedit bert.mgz" produces
GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context.

I thought maybe updating the NVidia card would help, but when I go to
their website and try to download NVidia Quadro NVS, there are only
Windows options to select as OS.

This is a Dell Precision T7500 preinstalled with RHEL 5.4.

About a year ago I installed freesurfer on virtually identical hardware
(the OS there was CentOS as a virtual machine under the Windows host), and
did not run into such a problem

Can you help me figure out why it's running into this problem and how to
fix it?

Thanks!
Dahlia.



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Re: [Freesurfer] [freesurfer] installation

[Douglas N Greve]

Is that file in that directory? What size is it? Do you have write 
permissions to that folder?

doug

Ignacio Letelier wrote:
> Hi all
>
> I'm a new freesurfer user and  I have some troubles installing the 
> program.
>
> after moving to
> cd /usr/local
>
> I typed *freesurfer-virtual:~>* tar xzvf 
> freesurfer-Linux---full.tar.gz
> replacing  -  with 
> freesurfer-Linux-centos4-stable-pub-v4.3.1
> I get  the following error message
>
>
> Cannot 
> >>/ open: No such file or directory
> />>/ 
> />>/ tar: Error is not recoverable: exiting now
> />>/ 
>
> />>/ tar: Child returned status 2
> />>/ 
> />>/ tar: Error exit delayed from previous errors
> /
>
> I don´t know exactly what I'm doing wrong, this may happen because I'm not in 
> the right directory or something?
> How can I get informnation about my Linux and Freesurfer software version./
>
> /
>
>
> Any help will be greatly appreciated, thanks in advance
>
> -- 
> Ignacio
> 
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] [freesurfer] installation

[Ignacio Letelier]

Hi all

I'm a new freesurfer user and  I have some troubles installing the program.

after moving to

cd /usr/local

I typed *freesurfer-virtual:~>* tar xzvf
freesurfer-Linux---full.tar.gz

replacing  -  with

freesurfer-Linux-centos4-stable-pub-v4.3.1

I get  the following error message

Cannot
>>* open: No such file or directory
*>>*
*>>* tar: Error is not recoverable: exiting now
*>>*
*>>* tar: Child returned status 2
*>>*
*>>* tar: Error exit delayed from previous errors
*
I don´t know exactly what I'm doing wrong, this may happen because I'm
not in the right directory or something?
How can I get informnation about my Linux and Freesurfer software version.*
*


Any help will be greatly appreciated, thanks in advance


-- 
Ignacio
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[Freesurfer] [freesurfer] installation failure

[Glen Lee]

 Dear freesurfer experts,
 I'm running into installation failure and can't quite figure this out (I'm
a novice Linux user too).
 It complains there is no such file or directory when I simply followed the
instruction by typing the command below in the /usr/local directory.

tar xzvf freesurfer-Linux-centos4-stable-pub-v4.5.0-full.tar.gz

Would anybody help me how to resolve this issue?
 Below is the error message and platform info. Many thanks!

 -GL
---
g...@ubuntu:/usr/local$ uname -a
Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC
2010 i686 GNU/Linux.


tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot
open: No such file or directory
freesurfer/average/surf/
tar: freesurfer/average/surf: Cannot mkdir: No such file or directory
freesurfer/average/surf/lh.sphere.reg
tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or
directory
freesurfer/average/surf/rh.sphere.reg
tar: freesurfer/average/surf/rh.sphere.reg: Cannot open: No such file or
directory
freesurfer/average/lh.atlas2002_simple.gcs
tar: freesurfer/average/lh.atlas2002_simple.gcs: Cannot open: No such file
or directory
freesurfer/average/rigidly_aligned_brain_template.tif
tar: freesurfer/average/rigidly_aligned_brain_template.tif: Cannot open: No
such file or directory
freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst
tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst: Cannot open: No
such file or directory
freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr
tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr: Cannot open: No
such file or directory
freesurfer/average/mni305.cor.subfov1.reg
tar: freesurfer/average/mni305.cor.subfov1.reg: Cannot open: No such file or
directory
freesurfer/average/rh.average.CURVATURE.tif
tar: freesurfer/average/rh.average.CURVATURE.tif: Cannot open: No such file
or directory
freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
tar:
freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs:
Cannot open: No such file or directory
freesurfer/average/mni_average_305.4dfp.img.rec
tar: freesurfer/average/mni_average_305.4dfp.img.rec: Cannot open: No such
file or directory
freesurfer/average/rh.average.curvature.filled.buckner40.tif
tar: freesurfer/average/rh.average.curvature.filled.buckner40.tif: Cannot
open: No such file or directory
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr
tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr: Cannot
open: No such file or directory
freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec
tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec: Cannot open:
No such file or directory
freesurfer/average/711-2C_as_mni_average_305.4dfp.mat
tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.mat: Cannot open: No
such file or directory
freesurfer/average/mni_average_305.4dfp.ifh
tar: freesurfer/average/mni_average_305.4dfp.ifh: Cannot open: No such file
or directory
freesurfer/average/mni305.cor.subfov2.reg
tar: freesurfer/average/mni305.cor.subfov2.reg: Cannot open: No such file or
directory
freesurfer/average/mni_average_305.4dfp.img
tar: freesurfer/average/mni_average_305.4dfp.img: Cannot open: No such file
or directory
freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh
tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh: Cannot open: No
such file or directory
freesurfer/average/face.gca
tar: freesurfer/average/face.gca: Cannot open: No such file or directory
freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs
tar:
freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs:
Cannot open: No such file or directory
freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec
tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec: Cannot open:
No such file or directory
freesurfer/average/rh.average.tif
tar: freesurfer/average/rh.average.tif: Cannot open: No such file or
directory
freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
tar:
freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs:
Cannot open: No such file or directory
freesurfer/average/711-2C_as_mni_average_305.4dfp.img
tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img: Cannot open: No
such file or directory
freesurfer/average/mni152.register.dat
tar: freesurfer/average/mni152.register.dat: Cannot open: No such file or
directory
freesurfer/average/RB_all_2007-08-08.gca
tar: freesurfer/average/RB_all_2007-08-08.gca: Cannot open: No such file or
directory
freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img
tar: freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img: Cannot
open: No such file or directory
freesurfer/average/mni305.cor.readme
tar: freesurfer/average/mni305.cor.readme: Cannot open: No such file or
directory
freesurfer/average/lh.at

[Freesurfer] Freesurfer installation on Ubuntu

[Miguel Burgaleta]

Hello FS experts,

I am trying to install FS on Ubuntu 9.04. I am testing the installation as
suggested in your website, and found the following message when attempting
to start the qdec application:

***
qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open
shared object file: No such file or directory
***

I am new to Linux as well, so I would really appreciate step-by-step
instructions to solve this issue.

Thanks in advance for your time,
Miguel
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Re: [Freesurfer] Freesurfer installation on Ubuntu desktop or server?

[Krish Subramaniam]

Yes, everything Rudolph said.
Also, the FreeSurfer we package for Ubuntu is actually a CentOS build  
because Ubuntu is a flavor of linux like  CentOS and since FreeSurfer  
package is self-contained everything should work once you un-tar-gz.

The only things we don't bundle are X server and OpenGL which are a  
must have for a functioning FreeSurfer system. So you should choose  
whichever Ubuntu offers X and OpenGL.

On Sep 9, 2009, at 11:17 PM, Rudolph Pienaar wrote:

> Burcu Ays,en Ürgen wrote:
>> Hi all,
>>
>> If one installs Freesurfer on Ubuntu, should he/she prefer the  
>> desktop
>> version of Ubuntu or server edition? Does it matter?
>>
> From FreeSurfer's perspective, it doesn't matter all that much if at
> all -- depends more on what other tasks you want the machine to do.  
> The
> Ubuntu kernel shipped with the 'server' edition is optimized towards a
> different set of constraints than the 'desktop' edition (server:  
> better
> support for virtualization, 64GB memory addressing for 32-bit systems,
> etc; desktop: pre-empting turned on for quicker desktop response, 32- 
> bit
> version can only address 4GB of memory, lots of user-space apps like
> openoffice, firefox, etc.).
>
> Other than that, each offers different set of base installed apps. The
> "server" edition comes out-of-the-box with a lot more "servers" than  
> the
> "desktop" edition. In fact, the server edition doesn't even install  
> X11
> by default.
>
> Of course, nothing prevents you from installing all the server apps in
> the desktop edition, or adding all the desktop tools in the server
> edition post-install -- at which point other than different kernel
> optimizations there's little difference.
>
> Personally, I'd install the desktop version and add whatever  
> additional
> servers I might need afterwards -- you'll be up and running FS a lot
> quicker.
>
> -- 
> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> 149 (2301) 13th Street, Charlestown, MA 02129 USA
>
> ___
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>
>


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Re: [Freesurfer] Freesurfer installation on Ubuntu desktop or server?

[Rudolph Pienaar]

Burcu Ays,en Ürgen wrote:
> Hi all,
>
> If one installs Freesurfer on Ubuntu, should he/she prefer the desktop 
> version of Ubuntu or server edition? Does it matter?
>
 From FreeSurfer's perspective, it doesn't matter all that much if at 
all -- depends more on what other tasks you want the machine to do. The 
Ubuntu kernel shipped with the 'server' edition is optimized towards a 
different set of constraints than the 'desktop' edition (server: better 
support for virtualization, 64GB memory addressing for 32-bit systems, 
etc; desktop: pre-empting turned on for quicker desktop response, 32-bit 
version can only address 4GB of memory, lots of user-space apps like 
openoffice, firefox, etc.).

Other than that, each offers different set of base installed apps. The 
"server" edition comes out-of-the-box with a lot more "servers" than the 
"desktop" edition. In fact, the server edition doesn't even install X11 
by default.

Of course, nothing prevents you from installing all the server apps in 
the desktop edition, or adding all the desktop tools in the server 
edition post-install -- at which point other than different kernel 
optimizations there's little difference.

Personally, I'd install the desktop version and add whatever additional 
servers I might need afterwards -- you'll be up and running FS a lot 
quicker.

-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA

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[Freesurfer] Freesurfer installation on Ubuntu desktop or server?

[Burcu Ayşen Ürgen]

Hi all,

If one installs Freesurfer on Ubuntu, should he/she prefer the desktop
version of Ubuntu or server edition? Does it matter?

Thank you,

Burcu Aysen Urgen.
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Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

[dahlia]

autoredraw on does not help.

i don't know whether i'm using vmware or virtualbox.

can anyone comment on how to check that and whether this should solve the
problem?

thanks!!!

> Can you post the output of dmesg command?
> Are you using vmware? TkSurfer works fine in Virtualbox (2.1.4) but I'm
> not
> sure it'll do in current vmware. If you are using it I suggest you to
> migrate your virtual machine to VirtualBox: http://www.virtualbox.org/
>
> Have you tried setting the autoredraw on in tksurfer interface?
>
> -
> Pedro Paulo de M. Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> --- Novo Netfilter 3.0 www.netfilter.com.br
>
>
>
> 2009/4/1 
>>
>> that did not work.
>> (thanks for trying, and yes, i'm using tcsh)
>>
>> > If you are using tcsh
>> >
>> > setenv doublebufferflag 1
>> >
>> > in bash
>> >
>> > export doublebufferflag=1
>> >
>> > ---
>> > Pedro Paulo de M. Oliveira Junior
>> > Diretor de Operações
>> > Netfilter & SpeedComm Telecom
>> > --- Novo Netfilter 3.0 www.netfilter.com.br
>> >
>> >
>> >
>> > On 1 de abril de 2009 14:55,  wrote:
>> >
>> >> Hi,
>> >>
>> >> I've installed freesurfer on my Stanford linux machine, and while
>> >> checking
>> >> it can see subject bert in tkmedit. However, tksurfer isn't drawing
>> in
>> >> its
>> >> window, and there's an error message
>> >>
>> >> surfer: ### redraw failed: no gl window open
>> >>
>> >> The installation is over Fedora Core 6 (build x86_64)
>> >>
>> >> How do I correct this?
>> >>
>> >> Thanks!
>> >> Dahlia.
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >
>>
>

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Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

[Pedro Paulo de Magalhães Oliveira Junior]

Can you post the output of dmesg command?
Are you using vmware? TkSurfer works fine in Virtualbox (2.1.4) but I'm not
sure it'll do in current vmware. If you are using it I suggest you to
migrate your virtual machine to VirtualBox: http://www.virtualbox.org/

Have you tried setting the autoredraw on in tksurfer interface?

-
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br



2009/4/1 
>
> that did not work.
> (thanks for trying, and yes, i'm using tcsh)
>
> > If you are using tcsh
> >
> > setenv doublebufferflag 1
> >
> > in bash
> >
> > export doublebufferflag=1
> >
> > ---
> > Pedro Paulo de M. Oliveira Junior
> > Diretor de Operações
> > Netfilter & SpeedComm Telecom
> > --- Novo Netfilter 3.0 www.netfilter.com.br
> >
> >
> >
> > On 1 de abril de 2009 14:55,  wrote:
> >
> >> Hi,
> >>
> >> I've installed freesurfer on my Stanford linux machine, and while
> >> checking
> >> it can see subject bert in tkmedit. However, tksurfer isn't drawing in
> >> its
> >> window, and there's an error message
> >>
> >> surfer: ### redraw failed: no gl window open
> >>
> >> The installation is over Fedora Core 6 (build x86_64)
> >>
> >> How do I correct this?
> >>
> >> Thanks!
> >> Dahlia.
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >
>
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Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

[dahlia]

that did not work.
(thanks for trying, and yes, i'm using tcsh)

> If you are using tcsh
>
> setenv doublebufferflag 1
>
> in bash
>
> export doublebufferflag=1
>
> ---
> Pedro Paulo de M. Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> --- Novo Netfilter 3.0 www.netfilter.com.br
>
>
>
> On 1 de abril de 2009 14:55,  wrote:
>
>> Hi,
>>
>> I've installed freesurfer on my Stanford linux machine, and while
>> checking
>> it can see subject bert in tkmedit. However, tksurfer isn't drawing in
>> its
>> window, and there's an error message
>>
>> surfer: ### redraw failed: no gl window open
>>
>> The installation is over Fedora Core 6 (build x86_64)
>>
>> How do I correct this?
>>
>> Thanks!
>> Dahlia.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>

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Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

[Pedro Paulo de Magalhães Oliveira Junior]

If you are using tcsh

setenv doublebufferflag 1

in bash

export doublebufferflag=1

---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br



On 1 de abril de 2009 14:55,  wrote:

> Hi,
>
> I've installed freesurfer on my Stanford linux machine, and while checking
> it can see subject bert in tkmedit. However, tksurfer isn't drawing in its
> window, and there's an error message
>
> surfer: ### redraw failed: no gl window open
>
> The installation is over Fedora Core 6 (build x86_64)
>
> How do I correct this?
>
> Thanks!
> Dahlia.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] Freesurfer installation: tksurfer not drawing

[dahlia]

Hi,

I've installed freesurfer on my Stanford linux machine, and while checking
it can see subject bert in tkmedit. However, tksurfer isn't drawing in its
window, and there's an error message

surfer: ### redraw failed: no gl window open

The installation is over Fedora Core 6 (build x86_64)

How do I correct this?

Thanks!
Dahlia.
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Re: [Freesurfer] Freesurfer Installation on Ubuntu 6.06

[Nick Schmansky]

Hema,

What is your DISPLAY environment variable set to?  That is, what is the
output of:

echo $DISPLAY

it should be something like:

:0.0


Nick


On Sun, 2008-12-14 at 17:16 -0500, Hemalatha Sampath wrote:
> Hi,
> 
> I am trying to install freesurfer on Ubuntu 6.06 32 bit processor machine. I 
> have downloaded the centos4-stable-pib-v4.1.0 and followed the installation 
> instructions. I am installing it through remote login via ssh. 
> During testing the installation by executing the tkmedit bert sample-001.mgz, 
> the error message that is provided:
> GLUT: Fatal Error in tkmedit.bin: could not open display: 
> 
> When I do cat /etc/debian_version, I receive testing/unstable.
> 
> Any help would be highly appreciated.
> 
> Thanks,
> Hema
> 
> 
> 
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[Freesurfer] Freesurfer Installation on Ubuntu 6.06

[Hemalatha Sampath]

Hi,

I am trying to install freesurfer on Ubuntu 6.06 32 bit processor machine. I 
have downloaded the centos4-stable-pib-v4.1.0 and followed the installation 
instructions. I am installing it through remote login via ssh. 
During testing the installation by executing the tkmedit bert sample-001.mgz, 
the error message that is provided:
GLUT: Fatal Error in tkmedit.bin: could not open display: 

When I do cat /etc/debian_version, I receive testing/unstable.

Any help would be highly appreciated.

Thanks,
Hema



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Re: [Freesurfer] Freesurfer Installation Problem

[Nick Schmansky]

Jaakko,

The message about the missing talairach.xfm file can be ignored (unless
things stop completely and issue an error message).  The code performs a
relative path search to find the file if it doesnt find it in the hard-
coded path (a historical remnant).

About the Tcl problem, which Linux OS variant is being used?  Freesurfer
does include Tcl/Tk/Tix/BLT (in $FREESURFER_HOME/lib/tcltktixblt) and
'tksurfer' is actually a wrapper script which performs the setup to use
those libs, then calls tksurfer.bin.  This is intended to prevent
conflicts with other Tcl/Tk installations.

Maybe you have an existing Tcl/Tk installation that is conflicting and
not handled by our wrapper script.  Before sourcing the freesurfer setup
file (SetupFreeSurferEnv.csh), can you type the following:

  env | grep TCL
  env | grep LD_LIBRARY_PATH
  which tclsh
  which tclsh8.4

This will tell you if you have an existing installation.

Also, are you trying to run tksurfer locally, or over a network
connection, like VNC?

Nick


On Fri, 2007-01-05 at 12:46 -0800, Jaakko Karras wrote:
> I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server
> running Fedora Core 3 (w/ x86_64), but ran into the following error
> upon testing the installation with the command "tkmedit bert
> orig.mgz":
> 
> $ tkmedit bert orig.mgz
>   Talairach
> transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm 
> does not exist ...
> Loading tal xfm
> file 
> /home/fmri/fmrihome/dti/software/freesurfer/subjects/bert/mri/transforms/talairach.xfm
> 
> The setup script ran flawlessly, producing the following output:
> 
> $ source SetUpFreeSurfer.csh
>  freesurfer-Linux-centos4-stable-pub-v3.0.4 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /home/fmri/fmrihome/dti/software/freesurfer
> FSFAST_HOME /home/fmri/fmrihome/dti/software/freesurfer/fsfast
> SUBJECTS_DIR/home/fmri/fmrihome/dti/software/freesurfer/subjects
> MNI_DIR /home/fmri/fmrihome/dti/software/freesurfer/mni
> GSL_DIR /home/fmri/fmrihome/dti/software/freesurfer/lib/gsl
> FSL_DIR /home/fmri/fmrihome/fsl
> 
> I was able to locate the "missing" talairach.xfm file in the
> appropriate directory.
> 
> On another note, I run into the following tcl/tk error when running
> tksurfer:
> 
> Tk_Init failed: Can't find a usable tk.tcl in the following
> directories: 
> /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 
> /home/
> fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 ./lib/tk8.4 
> ./li
> b/tk8.4 ./library ./library ./tk8.4.6/library ./tk8.4.6/library
> 
> /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: 
> ca
> n't access "::tk::Priv.:::171.65.48.253:0": parent namespace
> doesn't exist
> can't access "::tk::Priv.:::171.65.48.253:0": parent namespace
> doesn't exist
> while executing
> "upvar #0 ::tk::Priv.:::171.65.48.253:0 ::tk::Priv"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 upvar #0 ::tk::Priv.$disp ::tk::Priv"
> (procedure "tk::ScreenChanged" line 9)
> invoked from within
> "tk::ScreenChanged [winfo screen .]"
> (file
> "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
> /tk.tcl" line 277)
> invoked from within
> "source 
> /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
> .tcl"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list source $file]"
> /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: 
> ca
> n't import command "mc": already exists
> can't import command "mc": already exists
> while executing
> "namespace import ::msgcat::mc"
> (in namespace eval "::tk::msgcat" script line 21)
> invoked from within
> "namespace eval msgcat {
> namespace export mc mcmax
> if {[interp issafe] || [catch {package require msgcat}]} {
> # The msgcat..."
> (in namespace eval "::tk" script line 3)
> invoked from within
> "namespace eval ::tk {
> # Set up the msgcat commands
> namespace eval msgcat {
> namespace export mc mcmax
> if {[interp issafe] || [..."
> (file
> "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
> /tk.tcl" line 20)
> invoked from within
> "source 
> /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
> .tcl"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list source $file]"
> 
> 
> This probably means that tk wasn't installed properly.
> 
> 
> I run into the same error when opening the FSL 3.3 GUI, so I assume
> the error from FreeSurfer is related. I understood that the latest
> FreeSurfer is packaged with the required tcl/tk libraries, so this
> shouldn't be an issue. Any thoughts?
> 
> Note: I also installed the standard CentOS 4 (non 64 bit)
> distribution, but encountered the same problems.

[Freesurfer] Freesurfer Installation Problem

[Jaakko Karras]

I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server running 
Fedora Core 3 (w/ x86_64), but ran into the following error upon testing the 
installation with the command "tkmedit bert orig.mgz":

$ tkmedit bert orig.mgz
  Talairach transform 
/autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not 
exist ...
Loading tal xfm file 
/home/fmri/fmrihome/dti/software/freesurfer/subjects/bert/mri/transforms/talairach.xfm

The setup script ran flawlessly, producing the following output:

$ source SetUpFreeSurfer.csh
 freesurfer-Linux-centos4-stable-pub-v3.0.4 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/fmri/fmrihome/dti/software/freesurfer
FSFAST_HOME /home/fmri/fmrihome/dti/software/freesurfer/fsfast
SUBJECTS_DIR /home/fmri/fmrihome/dti/software/freesurfer/subjects
MNI_DIR /home/fmri/fmrihome/dti/software/freesurfer/mni
GSL_DIR /home/fmri/fmrihome/dti/software/freesurfer/lib/gsl
FSL_DIR /home/fmri/fmrihome/fsl

I was able to locate the "missing" talairach.xfm file in the appropriate 
directory.

On another note, I run into the following tcl/tk error when running tksurfer:

Tk_Init failed: Can't find a usable tk.tcl in the following directories: 
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 /home/
fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 ./lib/tk8.4 ./li
b/tk8.4 ./library ./library ./tk8.4.6/library ./tk8.4.6/library

/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca
n't access  "::tk::Priv.:::171.65.48.253:0": parent namespace doesn't exist
can't access "::tk::Priv.:::171.65.48.253:0": parent namespace doesn't exist
while executing
"upvar #0 ::tk::Priv.:::171.65.48.253:0 ::tk::Priv"
("uplevel" body line 1)
invoked from within
"uplevel #0 upvar #0 ::tk::Priv.$disp ::tk::Priv"
(procedure "tk::ScreenChanged" line 9)
invoked from within
"tk::ScreenChanged [winfo screen .]"
(file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
/tk.tcl" line 277)
invoked from within
"source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source  $file]"
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca
n't import command "mc": already exists
can't import command "mc": already exists
while executing
"namespace import ::msgcat::mc"
(in namespace eval "::tk::msgcat" script line 21)
invoked from within
"namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [catch {package require msgcat}]} {
# The msgcat..."
(in namespace eval "::tk" script line 3)
invoked from within
"namespace eval ::tk {
# Set up the msgcat commands
namespace eval msgcat {
namespace  export mc mcmax
if {[interp issafe] || [..."
(file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
/tk.tcl" line 20)
invoked from within
"source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"


This probably means that tk wasn't installed properly.


I run into the same error when opening the FSL 3.3 GUI, so I assume the error 
from FreeSurfer is related. I understood that the latest FreeSurfer is packaged 
with the required tcl/tk libraries, so this shouldn't be an issue. Any thoughts?

Note: I also installed the standard CentOS 4 (non 64 bit) distribution, but 
encountered the same  problems.

Thanks,
Jaakko
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Re: [Freesurfer] freesurfer installation problems

[Bruce Fischl]

Hi Chacko,

FREESURFER_HOME is an environment variable you need to set to point to 
the place that you intalled FreeSurfer.


Bruce
On Tue, 16 May 2006, Chacko Cherian 
wrote:



Hello all,

I am having some trouble in using the freesurfer
version I had downloaded.The FREESURFER_HOME file is
missing and so I cannot source or setenv anytime I
want to use it.Do I need to tar and unzip again or is
there any other way?
Thanks in advance

Chacko.

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[Freesurfer] freesurfer installation problems

[Chacko Cherian]

Hello all,

I am having some trouble in using the freesurfer
version I had downloaded.The FREESURFER_HOME file is
missing and so I cannot source or setenv anytime I
want to use it.Do I need to tar and unzip again or is
there any other way?
Thanks in advance

Chacko.

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