[Freesurfer] Freeview
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] Freeview
External Email - Use Caution -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 3:02 Subject: Re: [Freesurfer] Freeview To: fsbuild 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 () 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 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] Freeview
External Email - Use Caution 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 () 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 wrote: > > External Email - Use Caution > > > > -- Forwarded message - > De: Juan Rivas > Date: vie., 12 jul. 2019 a las 3:02 > Subject: Re: [Freesurfer] Freeview > To: fsbuild > > > 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 () > 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 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] Fwd: Freeview
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 Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: Cc: 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 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 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 () 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 wrote: > > External Email - Use Caution > > > > -- Forwarded message - > De: Juan Rivas > Date: vie., 12 jul. 2019 a las 3:02 > Subject: Re: [Freesurfer] Freeview > To: fsbuild > > > 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 () > 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 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] freeview
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 Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Fwd: Freeview
External Email - Use Caution 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 Date: lun., 15 jul. 2019 a las 15:19 Subject: Re: [Freesurfer] Fwd: Freeview To: Cc: 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 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 Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: Cc: 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 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 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 () 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 wrote: > > External Email - Use Caution > > > > -- Forwarded message - > De: Juan Rivas > Date: vie., 12 jul. 2019 a las 3:02 > Subject: Re: [Freesurfer] Freeview > To: fsbuild > > > 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 () > 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 > > 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? &
[Freesurfer] Fwd: freeview
External Email - Use Caution It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/freesurfer/bin/freeview But when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$ ldd freeview | grep not ldd: ./freeview: No such file or directory. Thank you for your help, JC. -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 6:57 Subject: freeview To: 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 Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: freeview
External Email - Use Caution libgfortran.so.3. No found. I día the fortran step as you indicated yo me. Thanks again, JC. -- Mensaje reenviado - De: fsbuild Fecha: El lun, 15 de jul. de 2019 a las 17:09 Asunto: Re: [Freesurfer] freeview Para: Cc: Did you try, $ ldd /usr/local/freesurfer/bin/freeview | grep not ? - R. On Jul 12, 2019, at 08:42, Juan Rivas wrote: External Email - Use Caution It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/freesurfer/bin/freeview But when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$ ldd freeview | grep not ldd: ./freeview: No such file or directory. Thank you for your help, JC. -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 6:57 Subject: freeview To: 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 Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. ___ 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] freeview
External Email - Use Caution I try again with fortran, uploaded it again, and now I get this message: jcrn12@jcrn12-VirtualBox:~$ freeview This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) Best regards, JC. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: freeview
External Email - Use Caution Have you found any solution? Is it possible to bring my computer to you as a way to solve the problem under your supervision? Thanks a lot. JC. -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 10:50 Subject: freeview To: I try again with fortran, uploaded it again, and now I get this message: jcrn12@jcrn12-VirtualBox:~$ freeview This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) Best regards, JC. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freeview
External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* I have installed fortran and update libx11, then I tried freeview and I get this message: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Could you please help me? Thanks, JC. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Freeview
External Email - Use Caution Hello, I am working with Ubuntu 18. I did what you asked to me, but the results are the same: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install qt5-default qtcreatorReading package lists... DoneBuilding dependency tree Reading state information... Doneqtcreator is already the newest version (4.5.2-3ubuntu2).qt5-default is already the newest version (5.9.5+dfsg-0ubuntu2.1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libqt5x11extras5-devReading package lists... DoneBuilding dependency tree Reading state information... Donelibqt5x11extras5-dev is already the newest version (5.9.5-0ubuntu1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Then, I tried: *jcrn12@jcrn12-VirtualBox:~$ libxcb.so.1 => /lib64/libxcb.so.1 bash: /lib64/libxcb.so.1: Permission denied* What could be the next step? Thanks a lot, JC. -- Forwarded message - De: fsbuild Date: mar., 16 jul. 2019 a las 10:38 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, You can try installing the following, $ sudo apt-get install qt5-default qtcreator $ sudo apt-get install libqt5x11extras5-dev Are you working on Ubuntu 18 ? - R. On Jul 12, 2019, at 22:29, Juan Rivas wrote: External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* I have installed fortran and update libx11, then I tried freeview and I get this message: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Could you please help me? Thanks, 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] Fwd: Fwd: Freeview
External Email - Use Caution That was the systemś answer: jcrn12@jcrn12-VirtualBox:~$ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms libqeglfs.so libqminimalegl.so libqoffscreen.so libqxcb.so libqlinuxfb.so libqminimal.so libqvnc.so jcrn12@jcrn12-VirtualBox:~$ export QT_DEBUG_PLUGINS=1 jcrn12@jcrn12-VirtualBox:~$ freeview QFactoryLoader::QFactoryLoader() checking directory path "/usr/local/freesurfer/bin/platforms" ... This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) -- Forwarded message - De: fsbuild Date: mar., 16 jul. 2019 a las 14:07 Subject: Re: [Freesurfer] Fwd: Freeview To: Cc: See if you have the following directory with the plugins libraries, $ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms There should be a libqxcb.so listed in that directory if you have them. Also try setting the following in your environment $ export QT_DEBUG_PLUGINS=1 - then try running freeview again and see what it reports. - R. On Jul 16, 2019, at 11:55, Juan Rivas wrote: External Email - Use Caution Hello, I am working with Ubuntu 18. I did what you asked to me, but the results are the same: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install qt5-default qtcreatorReading package lists... DoneBuilding dependency tree Reading state information... Doneqtcreator is already the newest version (4.5.2-3ubuntu2).qt5-default is already the newest version (5.9.5+dfsg-0ubuntu2.1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libqt5x11extras5-devReading package lists... DoneBuilding dependency tree Reading state information... Donelibqt5x11extras5-dev is already the newest version (5.9.5-0ubuntu1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Then, I tried: *jcrn12@jcrn12-VirtualBox:~$ libxcb.so.1 => /lib64/libxcb.so.1 bash: /lib64/libxcb.so.1: Permission denied* What could be the next step? Thanks a lot, JC. -- Forwarded message - De: fsbuild Date: mar., 16 jul. 2019 a las 10:38 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, You can try installing the following, $ sudo apt-get install qt5-default qtcreator $ sudo apt-get install libqt5x11extras5-dev Are you working on Ubuntu 18 ? - R. On Jul 12, 2019, at 22:29, Juan Rivas wrote: External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* I have installed fortran and update libx11, then I tried freeview and I get this message: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Could you please help me? Thanks, 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] Fwd: Fwd: Fwd: Freeview {Disarmed}
External Email - Use Caution Hello, this is the message I get: $ ls /usr/local/freesurfer/bin/platforms ls: cannot access '/usr/local/freesurfer/bin/platforms': No such file or directory $ sudo cd /usr/local/freesurfer/bin [sudo] password for jcrn12: sudo: cd: command not found $ Thank you, JC. -- Forwarded message - De: fsbuild Date: mar., 16 jul. 2019 a las 16:25 Subject: Re: [Freesurfer] Fwd: Fwd: Freeview To: Cc: OK, please check to see if this directory exists, $ ls /usr/local/freesurfer/bin/platforms If it does exist, then please let us know what is there with a repply email. But I expect that it does not exist and ls will report there is no such platforms directory.. If the directory does not exist, then go to the freesurfer bin directory and create a soft link to point to the Qt platforms subdirectory, $ sudo cd /usr/local/freesurfer/bin $ sudo ln -s /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms platforms If you create the link, then try running freeview again. - R. On Jul 13, 2019, at 03:33, Juan Rivas wrote: External Email - Use Caution That was the systemś answer: jcrn12@jcrn12-VirtualBox:~$ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms libqeglfs.so libqminimalegl.so libqoffscreen.so libqxcb.so libqlinuxfb.so libqminimal.so libqvnc.so jcrn12@jcrn12-VirtualBox:~$ export QT_DEBUG_PLUGINS=1 jcrn12@jcrn12-VirtualBox:~$ freeview QFactoryLoader::QFactoryLoader() checking directory path "/usr/local/freesurfer/bin/platforms" ... This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) -- Forwarded message - De: fsbuild Date: mar., 16 jul. 2019 a las 14:07 Subject: Re: [Freesurfer] Fwd: Freeview To: Cc: See if you have the following directory with the plugins libraries, $ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms There should be a libqxcb.so listed in that directory if you have them. Also try setting the following in your environment $ export QT_DEBUG_PLUGINS=1 - then try running freeview again and see what it reports. - R. On Jul 16, 2019, at 11:55, Juan Rivas wrote: External Email - Use Caution Hello, I am working with Ubuntu 18. I did what you asked to me, but the results are the same: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install qt5-default qtcreatorReading package lists... DoneBuilding dependency tree Reading state information Doneqtcreator is already the newest version (4.5.2-3ubuntu2).qt5-default is already the newest version (5.9.5+dfsg-0ubuntu2.1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libqt5x11extras5-devReading package lists... DoneBuilding dependency tree Reading state information... Donelibqt5x11extras5-dev is already the newest version (5.9.5-0ubuntu1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Then, I tried: *jcrn12@jcrn12-VirtualBox:~$ libxcb.so.1 => /lib64/libxcb.so.1 bash: /lib64/libxcb.so.1: Permission denied* What could be the next step? Thanks a lot, JC. -- Forwarded message - De: fsbuild Date: mar., 16 jul. 2019 a las 10:38 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, You can try installing the following, $ sudo apt-get install qt5-default qtcreator $ sudo apt-get install libqt5x11extras5-dev Are you working on Ubuntu 18 ? - R. On Jul 12, 2019, at 22:29, Juan Rivas wrote: External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem..Aborted (core dumped)* I have installed fortran and update libx11, then I tried freeview and I get this message: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find or load the Qt platform plugin "xcb"in "".Reinstalling the application may fix this problem.Aborted (core dumped)* Could you please help me? Thanks, JC. _
[Freesurfer] Tracula
External Email - Use Caution Hi, I am trying to make the recon with diffusion images for running tracula. I gave this command: set cmd = dt_recon set cmd = ($cmd --b $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvals set cmd = ($cmd --b $SUBJECTS_DIR/esq-15 hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvecs) set cmd = ($cmd --i $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/esq-15-hc_dwi.nii.gz) set cmd = ($cmd --s $SUBJECTS_DIR/esq-15-hc/) set cmd = ($cmd --o $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing) echo $cmd $cmd But ir marks two kinds of error: can´t fin bvals.dat or Eddy/Motion correct and stops. Could yo help me? Thanks, JC. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 7
External Email - Use Caution Thank you for your answer, I pursued your recommendations, and now the warning is that it can open file../COR-.info. What can I do? JC. El sáb., 5 oct. 2019 a las 12:00, escribió: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >1. Re: Curvature estimation from Hessian (LOSKE, PHILIPP (PGR)) >2. Segmentation faule recon-all (Backhausen, Lea) >3. Tracula (Juan Rivas) >4. Re: Tracula (Yendiki, Anastasia) >5. Question on Z-scoring (Nillo, Ryan Michael R) >6. ERROR gtmseg (Marina Fern?ndez) >7. Re: Question on Z-scoring (Greve, Douglas N.,Ph.D.) >8. Re: ERROR gtmseg (Greve, Douglas N.,Ph.D.) >9. Re: Segmentation faule recon-all (Greve, Douglas N.,Ph.D.) > 10. Vertex by Vertex Analysis (WON JONG CHWA) > 11. Re: question about aparcstats2table (Kiyotaka Nemoto) > 12. Brodmann area parcellation (sang ho shin) > 13. Errors running TRACULA (data attached) - valid frame numbers > (Mazzetti, C. (Cecilia)) > 14. Confidence interval for Cohen's d from gamma/rstd > (Caspar M. Schwiedrzik) > 15. Re: Errors running TRACULA (data attached) - validframe > numbers (Yendiki, Anastasia) > > > -- > > Message: 1 > Date: Fri, 4 Oct 2019 16:27:51 + > From: "LOSKE, PHILIPP (PGR)" > Subject: Re: [Freesurfer] Curvature estimation from Hessian > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > < > am0pr0402mb36506bb2f6a775be1acfc1f9e8...@am0pr0402mb3650.eurprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hi Bruce, > > thank you for your explanation. I think I might have an idea, why the > Hessian matrix works in this case, maybe you can confirm or correct me if > I'm wrong. Usually, if you're having a 2d surface in space, the principle > curvatures are the eigenvalues of the shape operator (which needs > calculation of first and second fundamental form), not the Hessian. Only in > the particular case of a vanishing gradient, the eigenvalues are the same > as those of the Hessian. F.e. for a quadratic function, the gradient > vanishes at the minimum (in 1d first derivative is zero). Since you're > modelling a quadratic function in a local neighborhood around each vertex, > its minimum lies at the vertex, is that correct? if this is so, then the > gradient should vanish and Hessian matrix should be fine and my confusion > is resolved :). In the literature I found just vague explanations, > sometimes mentioning the shape operator, sometimes the Hessian. I just want > to make sure I understand this process correctly. > > Cheers > Philipp > > > Date: Thu, 3 Oct 2019 10:03:52 -0400 (EDT) > > > Hi Philipp > > the Hessian is estimated at each vertex by doing a quadratic fit to the > local surface as the height function over the tangent plane of all the > vertices in a 2-neighborhood of that vertex. I'm not sure what the gradient > vanishing is about, but the curvatures are just the eigenvalues of the > Hessian, so I don't think the gradient has anything to do with it. Not that > we also have some discrete tools for computing curvature > > make sense? > cheers > Bruce > On Thu, 3 Oct 2019, LOSKE, PHILIPP > (PGR) wrote: > > > > > External Email - Use Caution > > > > Hi, > > > > I am trying to understand how exactly FreeSurfer estimates the curvature > > values from the white surface. From the mailing lists I understood that > the > > white surface is modeled by fitting a second-order polynomial function > and > > curvatures are estimated from the Hessian matrix at each vertex (thank > you > > Bruce). However, I still have trouble to understand how this works in > > detail. First, as I understand it, curvature can only be derived from the > > Hessian if the gradient vanishes (why is this the case?), and from > > differential geometry, shouldn't instead the shape operator be &g
[Freesurfer] Tracula
External Email - Use Caution Hi, I have been trying to process my diffusion images, but I have a new problem: I wrote this dmrirc: # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/neuromod/rivas/imagenes/DICOM # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc # Subject IDs # set subjlist = (esq-15-hc) # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc set dcmlist = (dwi.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvecs.dat # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvals.dat # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: # set cvstempdir = $FREESURFER_HOME/subjects # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a
Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 13
External Email - Use Caution Hi, thank you for your answer. This file does exist, it contains 59.3 MB. JC. Message: 10 Date: Tue, 8 Oct 2019 22:23:11 + From: "Yendiki, Anastasia" Subject: Re: [Freesurfer] Tracula To: "freesurfer@nmr.mgh.harvard.edu" Message-ID: < bl0pr04mb4833da61a1a5e068536924af8a...@bl0pr04mb4833.namprd04.prod.outlook.com > Content-Type: text/plain; charset="us-ascii" Does this file exist? niiRead(): error opening file /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz Hi, I have been trying to process my diffusion images, but I have a new problem: I wrote this dmrirc: # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/neuromod/rivas/imagenes/DICOM # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc # Subject IDs # set subjlist = (esq-15-hc) # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc set dcmlist = (dwi.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvecs.dat # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvals.dat # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: # set cvstempdir = $FREESURFER_HOME/subjects # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples d
[Freesurfer] HippoAmyg
External Email - Use Caution *Hi, I runned the reconall of my images with FS60 with this command:* *shiraz[0]:NIFTI$ recon-all -i /autofs/cluster/neuromod/rivas/imagenes/NIFTI/sub-esq-02-en/anat/sub-esq-02-en_T1w.nii.gz -s /autofs/cluster/neuromod/rivas/subject-esq-02-en. There were no errors.* *Then I runned recon for hippocampus and amygdala with fsdev on Thu Aug 22 15:36:32 , with this command:* *segmentHA_T1.sh* *There were no errors. Then I identified and corrected manually the errors on the FS60 images.* *Then I run recon-all on fs60 without to touch hippo-amyg.* *Now, I am trying to make the hippo-amyg correction with this command:* *segmentHA_T1.sh on fsdev, and I got this error:* [shiraz:FS] (nmr-dev-env) segmentHA_T1.sh test1 # #@# Hippocampal Subfields processing (T1) left Fri Oct 11 17:20:27 EDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:11:17:20:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 1.23 1.35 1.67 run_segmentSubjectT1_autoEstimateAlveusML.sh /usr/local/freesurfer/dev/MCRv84/ test1 /cluster/neuromod/rivas/imagenes/FS 0. /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasMesh.gz /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasDump.mgz /usr/local/freesurfer/dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /usr/local/freesurfer/dev/bin/ 0 -- Setting up environment variables --- LD_LIBRARY_PATH is .:/lib64:/usr/local/freesurfer/dev/MCRv84//runtime/glnxa64:/usr/local/freesurfer/dev/MCRv84//bin/glnxa64:/usr/local/freesurfer/dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: Registering imageDump.mgz to hippocampal mask from ASEG $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz'... Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 0 Type Target : 3 ensure both FLOAT (3) Reordering axes in mov to better fit dst... ( -1 3 -2 ) Determinant after swap : 0.015625 Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) Dst: (1, 1, 1)mm and dim (37, 33, 61) Asserting both images: 1mm isotropic - reslicing Mov ... -- changing data type from 0 to 3 (noscale = 0)... -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels. -- Resampled: (1, 1, 1)mm and (37, 33, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - no Dst reslice necessary Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 0 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 0 ) - initial transform: Ti = [ ... 1.000 -0.9335110261151 0 1.00 -0.6030053897425 00 1.0 -1.9033167008449 000 1.0 ] - initial iscale: Ii =1 Resolution: 0 S( 37 33 61 ) T( 37 33 61 ) Iteration(f): 1 -- diff. to prev. transform: 17.9258 Iteration(f): 2 -- diff. to prev. transform: 13.3727 Iteration(f): 3 -- diff. to prev. transform: 12.6349 Iteration(f): 4 -- diff. to prev. transform: 0.963353 Iteration(f): 5 -- diff. to prev. transform: 0.23376 max it: 5 reached! - final transform: Tf = [ ... 0.9994502743718 -0.0309610775894 -0.0118558311665 0.1083605389283 0.0330356012422 0.9601637341023 0.2774783825190 -11.0026122646332 0.0027925093931 -0.2777175100517 0.9606587253036 3.8161835807274 000 1.0 ] - final iscale: If = 1 ** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * ** Final Transform: Adjusting final transform due to initial resampling (voxel or size changes) ... M = [ ... -0.2498625685929 -0.0029639577916 0.0077402693973 33.8236195063683 -0.0082589003105 0.0693695956298 -0.2400409335
Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 21
External Email - Use Caution Dear Juan Eugenio, thanks for your answer. I tried to do with the corrected images and wit the raw ones (before the correction), and I got the same error. Then I tried with two patients more and happened the same. I don´t know if it is due to the dev version we used, because the first time it worked very well. Best regards, JC. El dom., 13 oct. 2019 a las 12:01, escribió: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >1. HippoAmyg (Juan Rivas) >2. Learning dti processing tutorial (Renew Andrade) >3. Re: HippoAmyg (Iglesias Gonzalez, Juan E.) > > > -- > > Message: 1 > Date: Sat, 12 Oct 2019 16:02:28 -0400 > From: Juan Rivas > Subject: [Freesurfer] HippoAmyg > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > k+yph1ddvpw4o67qehmxfhvpem7gqob...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > *Hi, I runned the reconall of my images with FS60 with this command:* > > *shiraz[0]:NIFTI$ recon-all -i > > /autofs/cluster/neuromod/rivas/imagenes/NIFTI/sub-esq-02-en/anat/sub-esq-02-en_T1w.nii.gz > -s /autofs/cluster/neuromod/rivas/subject-esq-02-en. There were no errors.* > > *Then I runned recon for hippocampus and amygdala with fsdev on Thu Aug 22 > 15:36:32 , with this command:* > > *segmentHA_T1.sh* > > *There were no errors. Then I identified and corrected manually the errors > on the FS60 images.* > > *Then I run recon-all on fs60 without to touch hippo-amyg.* > > *Now, I am trying to make the hippo-amyg correction with this command:* > > *segmentHA_T1.sh on fsdev, and I got this error:* > > > > [shiraz:FS] (nmr-dev-env) segmentHA_T1.sh test1 > > # > > #@# Hippocampal Subfields processing (T1) left Fri Oct 11 17:20:27 EDT 2019 > > /usr/bin/time -o /dev/stdout > > @#@FSTIME 2019:10:11:17:20:27 run_segmentSubjectT1_autoEstimateAlveusML.sh > N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 1.23 > 1.35 1.67 > > run_segmentSubjectT1_autoEstimateAlveusML.sh > /usr/local/freesurfer/dev/MCRv84/ test1 /cluster/neuromod/rivas/imagenes/FS > 0. > /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasMesh.gz > /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasDump.mgz > /usr/local/freesurfer/dev/average/HippoSF/atlas/compressionLookupTable.txt > 0.05 left L-BFGS v21 /usr/local/freesurfer/dev/bin/ 0 > > -- > > Setting up environment variables > > --- > > LD_LIBRARY_PATH is > > .:/lib64:/usr/local/freesurfer/dev/MCRv84//runtime/glnxa64:/usr/local/freesurfer/dev/MCRv84//bin/glnxa64:/usr/local/freesurfer/dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: > > Registering imageDump.mgz to hippocampal mask from ASEG > > $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ > > > > --mov: Using imageDump.mgz as movable/source volume. > > --dst: Using > > /cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz > as target volume. > > --lta: Output transform as trash.lta . > > --mapmovhdr: Will save header adjusted movable as > imageDump_coregistered.mgz ! > > --sat: Using saturation 50 in M-estimator! > > > > reading source 'imageDump.mgz'... > > reading target > > '/cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz'... > > > > Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) > >Type Source : 0 Type Target : 3 ensure both FLOAT (3) > >Reordering axes in mov to better fit dst... ( -1 3 -2 ) > > Determinant after swap : 0.015625 > >Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) > >Dst: (1, 1, 1)mm and dim (37, 33, 61) > >Asserting both images: 1mm isotropic > > - reslicing Mov ... > >-- changing data type from 0 to 3 (noscale = 0)... > >-- Ori
Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 21
External Email - Use Caution Dear Juan Eugenio, thanks for your answer. I tried to do with the corrected images and wit the raw ones (before the correction), and I got the same error. Then I tried with two patients more and happened the same. I don´t know if it is due to the dev version we used, because the first time it worked very well. Best regards, JC. El dom., 13 oct. 2019 a las 12:01, escribió: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >1. HippoAmyg (Juan Rivas) >2. Learning dti processing tutorial (Renew Andrade) >3. Re: HippoAmyg (Iglesias Gonzalez, Juan E.) > > > -- > > Message: 1 > Date: Sat, 12 Oct 2019 16:02:28 -0400 > From: Juan Rivas > Subject: [Freesurfer] HippoAmyg > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > k+yph1ddvpw4o67qehmxfhvpem7gqob...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > *Hi, I runned the reconall of my images with FS60 with this command:* > > *shiraz[0]:NIFTI$ recon-all -i > > /autofs/cluster/neuromod/rivas/imagenes/NIFTI/sub-esq-02-en/anat/sub-esq-02-en_T1w.nii.gz > -s /autofs/cluster/neuromod/rivas/subject-esq-02-en. There were no errors.* > > *Then I runned recon for hippocampus and amygdala with fsdev on Thu Aug 22 > 15:36:32 , with this command:* > > *segmentHA_T1.sh* > > *There were no errors. Then I identified and corrected manually the errors > on the FS60 images.* > > *Then I run recon-all on fs60 without to touch hippo-amyg.* > > *Now, I am trying to make the hippo-amyg correction with this command:* > > *segmentHA_T1.sh on fsdev, and I got this error:* > > > > [shiraz:FS] (nmr-dev-env) segmentHA_T1.sh test1 > > # > > #@# Hippocampal Subfields processing (T1) left Fri Oct 11 17:20:27 EDT 2019 > > /usr/bin/time -o /dev/stdout > > @#@FSTIME 2019:10:11:17:20:27 run_segmentSubjectT1_autoEstimateAlveusML.sh > N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 1.23 > 1.35 1.67 > > run_segmentSubjectT1_autoEstimateAlveusML.sh > /usr/local/freesurfer/dev/MCRv84/ test1 /cluster/neuromod/rivas/imagenes/FS > 0. > /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasMesh.gz > /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasDump.mgz > /usr/local/freesurfer/dev/average/HippoSF/atlas/compressionLookupTable.txt > 0.05 left L-BFGS v21 /usr/local/freesurfer/dev/bin/ 0 > > -- > > Setting up environment variables > > --- > > LD_LIBRARY_PATH is > > .:/lib64:/usr/local/freesurfer/dev/MCRv84//runtime/glnxa64:/usr/local/freesurfer/dev/MCRv84//bin/glnxa64:/usr/local/freesurfer/dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: > > Registering imageDump.mgz to hippocampal mask from ASEG > > $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ > > > > --mov: Using imageDump.mgz as movable/source volume. > > --dst: Using > > /cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz > as target volume. > > --lta: Output transform as trash.lta . > > --mapmovhdr: Will save header adjusted movable as > imageDump_coregistered.mgz ! > > --sat: Using saturation 50 in M-estimator! > > > > reading source 'imageDump.mgz'... > > reading target > > '/cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz'... > > > > Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) > >Type Source : 0 Type Target : 3 ensure both FLOAT (3) > >Reordering axes in mov to better fit dst... ( -1 3 -2 ) > > Determinant after swap : 0.015625 > >Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) > >Dst: (1, 1, 1)mm and dim (37, 33, 61) > >Asserting both images: 1mm isotropic > > - reslicing Mov ... > >-- changing data type from 0 to 3 (noscale = 0)... > >-- Ori
[Freesurfer] Multiple comparisons
External Email - Use Caution I would like to know how the correction is made for multiple comparisons in the statistical analysis? We are using QDEC, with False Discovery Rate or Montecarlo Null-Z. Is there a better way to do that? Best, JC. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
