fslr error while using fsl functions inside Rstudio

[athanell]

Hello,
I installed fslr with devtools::install_github("muschellij2/fslr")
and also run the commands in the Installation.Rmd file
i.e
FSLDIR=/usr/local/fsl ; FSLSHARE=/usr/share/data; PATH=$PATH:${FSLDIR}/bin;
....
sudo cp -R ${FSLSHARE}/mni-structural-atlas/* ${FSLDIR}/data/atlases/ ; sudo cp -R ${FSLSHARE}/oxford-thalamic-connectivity-atlas/* ${FSLDIR}/data/atlases/ ; sudo cp -R ${FSLSHARE}/talairach-daemon-atlas/* ${FSLDIR}/data/atlases/;

I checked the folder /usr/local/fsl/bin and all files have been copied there from the folder /usr/lib/fsl/5.0/

But for some reason when I load the library

library(fslr)
Loading required package: oro.nifti
oro.nifti 0.8.0
Loading required package: neurobase

and try to run an fsl function like

fslmaths.help()
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
Error in system(cmd, intern = TRUE) : error in running command
In addition: Warning messages:
1: In get.fsl() : Setting fsl.path to /usr/local/fsl
2: In get.fsloutput() : Can't find FSLOUTPUTTYPE, setting to NIFTI_GZ

I get the error that the shared library libnewimage.so does not exist, even though it is in the /usr/local/fsl/bin folder.

When I run it from a terminal R I do not encounter this error.
Any ideas on how to resolve this problem?
Thank you

[muschellij2]

Can you try adding: export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH in your .bash_profile or .profile? John

…

On Fri, Sep 29, 2017 at 11:26 AM, Antonios Konstantinos < ***@***.***> wrote: Hello, I installed fslr with devtools::install_github("muschellij2/fslr") and also run the commands in the Installation.Rmd file i.e FSLDIR=/usr/local/fsl FSLSHARE=/usr/share/data PATH=$PATH:${FSLDIR}/bin .... sudo cp -R ${FSLSHARE}/mni-structural-atlas/* ${FSLDIR}/data/atlases/ sudo cp -R ${FSLSHARE}/oxford-thalamic-connectivity-atlas/* ${FSLDIR}/data/atlases/ sudo cp -R ${FSLSHARE}/talairach-daemon-atlas/* ${FSLDIR}/data/atlases/ I checked the folder /usr/local/fsl/bin and all files have been copied there from the folder /usr/lib/fsl/5.0/ But for some reason when I load the library library(fslr) Loading required package: oro.nifti oro.nifti 0.8.0 Loading required package: neurobase and try to run an fsl function like fslmaths.help() /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory Error in system(cmd, intern = TRUE) : error in running command In addition: Warning messages: 1: In get.fsl() : Setting fsl.path to /usr/local/fsl 2: In get.fsloutput() : Can't find FSLOUTPUTTYPE, setting to NIFTI_GZ I get the error that the shared library libnewimage.so does not exist, even though it is in the /usr/local/fsl/bin folder. When I run it from a terminal R I do not encounter this error. Any ideas on how to resolve this problem? Thank you — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABBnrt3_B-L5ljSaWaDxjg4KDNGGEcHEks5snQwfgaJpZM4Po1VE> .

[muschellij2]

Can you also print out the complete output from the command/error? John On Fri, Sep 29, 2017 at 11:29 AM, John Muschelli <muschellij2@gmail.com> wrote:

…

Can you try adding: export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH in your .bash_profile or .profile? John On Fri, Sep 29, 2017 at 11:26 AM, Antonios Konstantinos < ***@***.***> wrote: > Hello, > I installed fslr with devtools::install_github("muschellij2/fslr") > and also run the commands in the Installation.Rmd file > i.e > FSLDIR=/usr/local/fsl > FSLSHARE=/usr/share/data > PATH=$PATH:${FSLDIR}/bin > .... > sudo cp -R ${FSLSHARE}/mni-structural-atlas/* ${FSLDIR}/data/atlases/ > sudo cp -R ${FSLSHARE}/oxford-thalamic-connectivity-atlas/* > ${FSLDIR}/data/atlases/ > sudo cp -R ${FSLSHARE}/talairach-daemon-atlas/* ${FSLDIR}/data/atlases/ > > I checked the folder /usr/local/fsl/bin and all files have been copied > there from the folder /usr/lib/fsl/5.0/ > > But for some reason when I load the library > > library(fslr) > Loading required package: oro.nifti > oro.nifti 0.8.0 > Loading required package: neurobase > > and try to run an fsl function like > > fslmaths.help() > /usr/local/fsl/bin/fslmaths: error while loading shared libraries: > libnewimage.so: cannot open shared object file: No such file or directory > Error in system(cmd, intern = TRUE) : error in running command > In addition: Warning messages: > 1: In get.fsl() : Setting fsl.path to /usr/local/fsl > 2: In get.fsloutput() : Can't find FSLOUTPUTTYPE, setting to NIFTI_GZ > > I get the error that the shared library libnewimage.so does not exist, > even though it is in the /usr/local/fsl/bin folder. > > When I run it from a terminal R I do not encounter this error. > Any ideas on how to resolve this problem? > Thank you > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#4>, or mute the > thread > <https://github.com/notifications/unsubscribe-auth/ABBnrt3_B-L5ljSaWaDxjg4KDNGGEcHEks5snQwfgaJpZM4Po1VE> > . >

[athanell]

Hello John,

Thank you for the lightning fast answer.
Yes when I exported the path to the LD_LIBRARY_PATH , the problem was resolved