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Sorry - from your previous mail, I mistakenly thought “which freeview” returned /usr/local/bin/freeview. If you can reproduce what you did before to run freeview from the command line where it tells you that it was not finding libgfortran, then “which freeview” will likely tell you where the binary is. You should have already set FREESURFER_HOME to point to the freesurfer installation and then did the source of the shell init file (SetUpFreeSurfer.sh for bash or sh, SetUpFreeSurfer.csh for csh). See the wiki page here under setup and configuration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall%C2%A0; That should have put freeview in your PATH so that “which freeview” works. What you want to do is to cd into the directory where the freeview binary lives and run ldd on it. If “which freeview” returned /usr/local/bin/freeview then you could “cd /usr/local/bin” and from there directly run “ldd freeview | grep not”. - R. On Jul 12, 2019, at 07:32, Juan Rivas <jcrn12@gmail.com> wrote: External Email - Use Caution That is what happened:$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directoryJC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: lun., 15 jul. 2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: <freesurfer@nmr.mgh.harvard.edu>Cc: <jcrn12@gmail.com>Hello JC,Try this to see what libs are missing,$ ldd /usr/local/bin/freeview | grep not- R.On Jul 12, 2019, at 06:19, Juan Rivas <jcrn12@gmail.com> wrote: External Email - Use Caution Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18This is the message I get:$ freeviewsh: 8: freeview: not found$ which freeview $ /usr/local/bin/freeviewsh: 10: /usr/local/bin/freeview: not found$ which ldd/usr/bin/ldd$ ldd `which freeview` | grep notldd: missing file argumentsTry `ldd --help' for more information.Thank you very much,JC.El lun., 15 jul. 2019 a las 12:50, fsbuild (<fsbuild@contbay.com>) escribió:Hello Juan,For CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work then,$ sudo yum install libgfortran.x86_64For Ubuntu,$sudo apt-get install gfortranOne thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing....This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ.$ which freeview/usr/local/bin/freeview- then check you have the ldd command, $ which ldd/usr/bin/lddIf the above returned paths for freeview and ldd, then run the ldd command followed by the grep command to see what libraries are missing. Prior to doing the install of libgfortran above, it should list libgfortran is missing.$ ldd `which freeview` | grep notAlso it would be good to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.- R.On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12@gmail.com> wrote: External Email - Use Caution ---------- Forwarded message ---------De: Juan Rivas <jcrn12@gmail.com>Date: vie., 12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild <fsbuild@contbay.com>Hi, thank you for your answer.I did what you recommended to me, and I get this message:freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild@contbay.com>) escribió:Hello JC,Your machine could be missing the qt5 libraries/files.On Ubuntu linux you can try installing them with,$ sudo apt-get install qt5-default qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12@gmail.com> wrote: External Email - Use Caution Hello, I am trying to use freeview, but everytime I try I get this message:freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory.How can I fix it?Thanks a lot,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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It does not work: jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview /usr/local/freesurfer/bin/freeview jcrn12@jcrn12-VirtualBox:/usr/local/bin$ ldd freeview | grep not ldd: ./freeview: No such file or directory
JC ---------- Forwarded message --------- De: fsbuild fsbuild@contbay.com Date: lun., 15 jul. 2019 a las 15:19 Subject: Re: [Freesurfer] Fwd: Freeview To: freesurfer@nmr.mgh.harvard.edu Cc: jcrn12@gmail.com
Sorry - from your previous mail, I mistakenly thought “which freeview” returned /usr/local/bin/freeview.
If you can reproduce what you did before to run freeview from the command line where it tells you that it was not finding libgfortran, then “which freeview” will likely tell you where the binary is. You should have already set FREESURFER_HOME to point to the freesurfer installation and then did the source of the shell init file (SetUpFreeSurfer.sh for bash or sh, SetUpFreeSurfer.csh for csh). See the wiki page here under setup and configuration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall That should have put freeview in your PATH so that “which freeview” works.
What you want to do is to cd into the directory where the freeview binary lives and run ldd on it. If “which freeview” returned /usr/local/bin/freeview then you could “cd /usr/local/bin” and from there directly run “ldd freeview | grep not”.
- R.
On Jul 12, 2019, at 07:32, Juan Rivas jcrn12@gmail.com wrote:
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That is what happened: $ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory $ bash jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory JC. ---------- Forwarded message --------- De: fsbuild fsbuild@contbay.com Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: freesurfer@nmr.mgh.harvard.edu Cc: jcrn12@gmail.com
Hello JC,
Try this to see what libs are missing,
$ ldd /usr/local/bin/freeview | grep not
- R.
On Jul 12, 2019, at 06:19, Juan Rivas jcrn12@gmail.com wrote:
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Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18 This is the message I get:
$ freeview sh: 8: freeview: not found $ which freeview $ /usr/local/bin/freeview sh: 10: /usr/local/bin/freeview: not found $ which ldd /usr/bin/ldd $ ldd `which freeview` | grep not ldd: missing file arguments Try `ldd --help' for more information.
Thank you very much, JC.
El lun., 15 jul. 2019 a las 12:50, fsbuild (fsbuild@contbay.com) escribió:
Hello Juan,
For CentOS try: $ sudo yum install gcc-gfortran.x86_64 … if that does not work then, $ sudo yum install libgfortran.x86_64
For Ubuntu, $sudo apt-get install gfortran
One thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing....
This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ. $ which freeview /usr/local/bin/freeview
- then check you have the ldd command,
$ which ldd /usr/bin/ldd
If the above returned paths for freeview and ldd, then run the ldd command followed by the grep command to see what libraries are missing. Prior to doing the install of libgfortran above, it should list libgfortran is missing.
$ ldd `which freeview` | grep not
Also it would be good to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.
- R.
On Jul 15, 2019, at 12:39, Juan Rivas jcrn12@gmail.com wrote:
External Email - Use Caution---------- Forwarded message --------- De: Juan Rivas jcrn12@gmail.com Date: vie., 12 jul. 2019 a las 3:02 Subject: Re: [Freesurfer] Freeview To: fsbuild fsbuild@contbay.com
Hi, thank you for your answer. I did what you recommended to me, and I get this message: freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory. What could be the next step? JC.
El lun., 15 jul. 2019 a las 9:57, fsbuild (fsbuild@contbay.com) escribió:
Hello JC,
Your machine could be missing the qt5 libraries/files.
On Ubuntu linux you can try installing them with, $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev
On CentOS linux, $ sudo yum install qt-create qt-config.x86_64 $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel...x86_64
- R.
On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12@gmail..com jcrn12@gmail.com> wrote:
External Email - Use CautionHello, I am trying to use freeview, but everytime I try I get this message: freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory. How can I fix it? Thanks a lot, JC. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you need to run:
ldd /usr/local/freesurfer/bin/freeview | grep not
cheers Bruce On Fri, 12 Jul 2019, Juan Rivas wrote:
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It does not work:jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview /usr/local/freesurfer/bin/freeview jcrn12@jcrn12-VirtualBox:/usr/local/bin$ ldd freeview | grep not ldd: ./freeview: No such file or directory
JC ---------- Forwarded message --------- De: fsbuild fsbuild@contbay.com Date: lun., 15 jul. 2019 a las 15:19 Subject: Re: [Freesurfer] Fwd: Freeview To: freesurfer@nmr.mgh.harvard.edu Cc: jcrn12@gmail.com
Sorry - from your previous mail, I mistakenly thought “which freeview” returned /usr/local/bin/freeview. If you can reproduce what you did before to run freeview from the command line where it tells you that it was not finding libgfortran, then “which freeview” will likely tell you where the binary is. You should have already set FREESURFER_HOME to point to the freesurfer installation and then did the source of the shell init file (SetUpFreeSurfer.sh for bash or sh, SetUpFreeSurfer.csh for csh). See the wiki page here under setup andconfiguration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall That should have put freeview in your PATH so that “which freeview” works.
What you want to do is to cd into the directory where the freeview binary lives and run ldd on it. If “which freeview” returned /usr/local/bin/freeview then you could “cd /usr/local/bin” and from there directly run “ldd freeview | grep not”.
R.
On Jul 12, 2019, at 07:32, Juan Rivas <jcrn12@gmail.com> wrote:External Email - Use Caution
That is what happened: $ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory $ bash jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory JC. ---------- Forwarded message --------- De: fsbuild fsbuild@contbay.com Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: freesurfer@nmr.mgh.harvard.edu Cc: jcrn12@gmail.com
Hello JC, Try this to see what libs are missing,
$ ldd /usr/local/bin/freeview | grep not
- R. On Jul 12, 2019, at 06:19, Juan Rivas jcrn12@gmail.com wrote:
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Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18 This is the message I get:
$ freeview sh: 8: freeview: not found $ which freeview $ /usr/local/bin/freeview sh: 10: /usr/local/bin/freeview: not found $ which ldd /usr/bin/ldd $ ldd `which freeview` | grep not ldd: missing file arguments Try `ldd --help' for more information.
Thank you very much, JC.
El lun., 15 jul. 2019 a las 12:50, fsbuild (fsbuild@contbay.com) escribió: Hello Juan, For CentOS try: $ sudo yum install gcc-gfortran.x86_64 … if that does not work then, $ sudo yum install libgfortran.x86_64
For Ubuntu, $sudo apt-get install gfortran
One thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing....
This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ. $ which freeview /usr/local/bin/freeview
- then check you have the ldd command,
$ which ldd /usr/bin/ldd
If the above returned paths for freeview and ldd, then run the ldd command followed by the grep command to see what libraries are missing. Prior to doing the install of libgfortran above, it should list libgfortran is missing.
$ ldd `which freeview` | grep not
Also it would be good to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.
R.
On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12@gmail.com> wrote:External Email - Use Caution
---------- Forwarded message --------- De: Juan Rivas jcrn12@gmail.com Date: vie., 12 jul. 2019 a las 3:02 Subject: Re: [Freesurfer] Freeview To: fsbuild fsbuild@contbay.com
Hi, thank you for your answer.I did what you recommended to me, and I get this message:freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory. What could be the next step? JC.
El lun., 15 jul. 2019 a las 9:57, fsbuild (fsbuild@contbay.com) escribió: Hello JC, Your machine could be missing the qt5 libraries/files.
On Ubuntu linux you can try installing them with, $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev
On CentOS linux, $ sudo yum install qt-create qt-config.x86_64 $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel...x86_64
R.
On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12@gmail..com> wrote:External Email - Use Caution
Hello, I am trying to use freeview, but everytime I try I get this message:freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory. How can I fix it? Thanks a lot, JC. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
fsbuild -
Juan Rivas