External Email - Use Caution
Hello Karin, If you take a look at this page, https://surfer.nmr.mgh..harvard.edu/fswiki/CMake%C2%A0; you should see there is a link to a file makefile.wiki which you can download. Besides trying to run the cmake command for you to help with building Freesurfer, there are some notes in the makefile about what packages to install with “sudo yum install <package>” for CentOS/Redhat linux. So you could try installing those packages, and then also try using that makefile to run cmake and build freesurfer..- R.
On Nov 25, 2018, at 17:00, Karin Markenroth Bloch <karin.markenroth_bloch@med.lu.se> wrote: External Email - Use Caution Dear all,I’m afraid this is a very basic Linux question, but I am not that familiar with it. I downloaded and installed FSLVm7_64 on a Windows7 host. Installation went well, and if I type fsl in the terminal window, a GUI (a menu list) pops up.My first attempt was to click “BET”, select an input image and Run standard brain extraction using bet. Then I get the messages (see below):“ error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory” The libopenblas.so is in my /home/flsuser/Data directory. I tried installing it sudo yum install libopenblas.so, but get the reply “No package libopenblas.so available.” (see below) I have set the $FSLDIR variable : [fsluser@localhost Data]$ echo $FSLDIR /usr/local/fsl What can I do? Very grateful for help! YoursKarin ------------[fsluser@localhost ~]$ fsl/usr/local/fsl/bin/bet /home/fsluser/Data/s20181112-0601-00006-000001-01 /home/fsluser/Data/s20181112-0601-00006-000001-01_brain -f 0.5 -g 0/usr/local/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directoryFinished /home/fsluser[fsluser@localhost ~]$ cd Data/ [fsluser@localhost Data]$ lslibopenblas.so s20181112-0601-00006-000001-01.nii [fsluser@localhost Data]$ sudo yum install libopenblas.so[sudo] password for fsluser: Loaded plugins: fastestmirror, langpacksLoading mirror speeds from cached hostfile* base: mirror.hh.se* extras: mirror.hh.se* updates: mirror.hh.seNo package libopenblas.so available.Error: Nothing to do [fsluser@localhost Data]$ flirt /vflirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hello, many thanks for the answer! I have downloaded the makefile.wiki and installed the packages mentioned in it. However, I still don’t understand how can install the packages – they are on my computer, but the programs can’s “find” them. I guess there is either a path that needs to be set, or that they have to be installed/unpacked?
The ones I have problems with are: libopenblas.so – is in /home/flsuser/Data, linked to /usr/local/fsl/bin libXss.so.1 – is in /usr/lib/vmware-tools/lib64/libXss.so.1
The path is: PATH=/usr/local/fsl/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/fsluser/.local/bin:/home/fsluser/bin
Thanks for all help with these very basic questions! karin
---------------------------------------------------------------------------------------------------------------------------------- Karin Markenroth Bloch Site coordinator and researcher the national 7T facility Lund +46 708 322504 Karin.Markenroth@med.lu.semailto:Karin.Markenroth@med.lu.se Karin.Markenroth.Bloch (skype)
When you send emails to Lund University, we process your personal data in accordance with existing legislation. To find out more about the processing of your personal data, visit the Lund University website at: https://www.lunduniversity.lu.se/about/contact-us/processing-of-personal-dat...
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of fsbuild Sent: November 25, 2018 23:47 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error while loading shared libraries, FSLVm7_64
External Email - Use Caution Hello Karin,
If you take a look at this page, https://surfer.nmr.mgh.harvard.edu/fswiki/CMake you should see there is a link to a file makefile.wiki which you can download. Besides trying to run the cmake command for you to help with building Freesurfer, there are some notes in the makefile about what packages to install with “sudo yum install <package>” for CentOS/Redhat linux. So you could try installing those packages, and then also try using that makefile to run cmake and build freesurfer. . - R.
On Nov 25, 2018, at 17:00, Karin Markenroth Bloch <karin.markenroth_bloch@med.lu.semailto:karin.markenroth_bloch@med.lu.se> wrote:
External Email - Use Caution
Dear all, I’m afraid this is a very basic Linux question, but I am not that familiar with it.
I downloaded and installed FSLVm7_64 on a Windows7 host. Installation went well, and if I type fsl in the terminal window, a GUI (a menu list) pops up. My first attempt was to click “BET”, select an input image and Run standard brain extraction using bet. Then I get the messages (see below): “ error while loading shared libraries: libopenblas..so.0: cannot open shared object file: No such file or directory”
The libopenblas.so is in my /home/flsuser/Data directory. I tried installing it sudo yum install libopenblas.so, but get the reply “No package libopenblas.so available.” (see below)
I have set the $FSLDIR variable : [fsluser@localhost Data]$ echo $FSLDIR /usr/local/fsl
What can I do?
Very grateful for help!
Yours Karin
------------ [fsluser@localhost ~]$ fsl /usr/local/fsl/bin/bet /home/fsluser/Data/s20181112-0601-00006-000001-01 /home/fsluser/Data/s20181112-0601-00006-000001-01_brain -f 0.5 -g 0 /usr/local/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory Finished
/home/fsluser [fsluser@localhost ~]$ cd Data/
[fsluser@localhost Data]$ ls libopenblas.so s20181112-0601-00006-000001-01.nii
[fsluser@localhost Data]$ sudo yum install libopenblas.so [sudo] password for fsluser: Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.hh.sehttp://mirror..hh.se/ * extras: mirror.hh.sehttp://mirror.hh.se/ * updates: mirror.hh.sehttp://mirror.hh.se/ No package libopenblas.so available. Error: Nothing to do
[fsluser@localhost Data]$ flirt /v flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Karin, are you attempting to build or run freesurfer? Your original issue seems related to fsl, not freesurfer. I suggest consulting their help list to get FSLVm7_64 running correctly - https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Support
best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Karin Markenroth Bloch karin.markenroth_bloch@med.lu.se Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Sunday, November 25, 2018 at 8:06 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error while loading shared libraries, FSLVm7_64
External Email - Use Caution Hello, many thanks for the answer! I have downloaded the makefile.wiki and installed the packages mentioned in it. However, I still don’t understand how can install the packages – they are on my computer, but the programs can’s “find” them. I guess there is either a path that needs to be set, or that they have to be installed/unpacked?
The ones I have problems with are: libopenblas.so – is in /home/flsuser/Data, linked to /usr/local/fsl/bin libXss.so.1 – is in /usr/lib/vmware-tools/lib64/libXss.so.1
The path is: PATH=/usr/local/fsl/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/fsluser/.local/bin:/home/fsluser/bin
Thanks for all help with these very basic questions! karin
---------------------------------------------------------------------------------------------------------------------------------- Karin Markenroth Bloch Site coordinator and researcher the national 7T facility Lund +46 708 322504 Karin.Markenroth@med.lu.semailto:Karin.Markenroth@med.lu.se Karin.Markenroth.Bloch (skype)
When you send emails to Lund University, we process your personal data in accordance with existing legislation. To find out more about the processing of your personal data, visit the Lund University website at: https://www.lunduniversity.lu.se/about/contact-us/processing-of-personal-dat...
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of fsbuild Sent: November 25, 2018 23:47 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error while loading shared libraries, FSLVm7_64
External Email - Use Caution Hello Karin,
If you take a look at this page, https://surfer.nmr.mgh.harvard.edu/fswiki/CMake you should see there is a link to a file makefile.wiki which you can download. Besides trying to run the cmake command for you to help with building Freesurfer, there are some notes in the makefile about what packages to install with “sudo yum install <package>” for CentOS/Redhat linux. So you could try installing those packages, and then also try using that makefile to run cmake and build freesurfer. . - R.
On Nov 25, 2018, at 17:00, Karin Markenroth Bloch <karin.markenroth_bloch@med.lu.semailto:karin.markenroth_bloch@med.lu.se> wrote:
External Email - Use Caution
Dear all, I’m afraid this is a very basic Linux question, but I am not that familiar with it.
I downloaded and installed FSLVm7_64 on a Windows7 host. Installation went well, and if I type fsl in the terminal window, a GUI (a menu list) pops up. My first attempt was to click “BET”, select an input image and Run standard brain extraction using bet. Then I get the messages (see below): “ error while loading shared libraries: libopenblas..so.0: cannot open shared object file: No such file or directory”
The libopenblas.so is in my /home/flsuser/Data directory. I tried installing it sudo yum install libopenblas.so, but get the reply “No package libopenblas.so available.” (see below)
I have set the $FSLDIR variable : [fsluser@localhost Data]$ echo $FSLDIR /usr/local/fsl
What can I do?
Very grateful for help!
Yours Karin
------------ [fsluser@localhost ~]$ fsl /usr/local/fsl/bin/bet /home/fsluser/Data/s20181112-0601-00006-000001-01 /home/fsluser/Data/s20181112-0601-00006-000001-01_brain -f 0.5 -g 0 /usr/local/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory Finished
/home/fsluser [fsluser@localhost ~]$ cd Data/
[fsluser@localhost Data]$ ls libopenblas.so s20181112-0601-00006-000001-01.nii
[fsluser@localhost Data]$ sudo yum install libopenblas.so [sudo] password for fsluser: Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.hh.sehttp://mirror..hh.se/ * extras: mirror.hh.sehttp://mirror.hh.se/ * updates: mirror.hh.sehttp://mirror.hh.se/ No package libopenblas.so available. Error: Nothing to do
[fsluser@localhost Data]$ flirt /v flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Hoopes, Andrew -
Karin Markenroth Bloch