Dears, when I used the fslbet function, the mistake appeared, but I don't know what happened. My system is windows

Dear John,

Does fslr package include "flirt -applyisoxfm" function or other flags?

Thanks,
Kaiming

Hello John,
I am working on a project to do defacing, for which your library is being used in my script.
We have used your library without any error for several months since we installed it.
However, a following error suddenly recently appears when I run functions such as fslsmooth and CT_Skull_Strip_robust in fslr, even if fslr is sucessfully loaded in R.

smooth = fslsmooth(thresh.img, sigma = 0.5, retimg=TRUE)#sigma value to control to be soother

fslmaths "/tmp/Rtmpz4mcgw/file3897145cb153.nii.gz" -s 0.5 "/tmp/Rtmpz4mcgw/file389710b12b8f";

Error in (function (fname, onefile = TRUE, gzipped = TRUE, verbose = FALSE, :
Not all data was read in: should be length 34078720 but only 32156 was read in!

Do you know why this error occurs and how should I fix it?
Are there any requirements for installing particular versions of associated R packages to avoid this error in fslr?
Any advice will be great help!
Thanks,
Tingyu

Hi all,

I have struggled with these problems several days.Hope you can help me.
When I use the function fsl_biascorrect,it failed and says:

fast    -B --nopve --out="/tmp/Rtmpq11Eub/file2cc6356910d4" "/tmp/Rtmpq11Eub/file2cc679823327.nii.gz";

fast: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
cannot remove file '/tmp/Rtmpq11Eub/file2cc6356910d4_seg.nii.gz', reason 'No such file or directory'cannot rename file '/tmp/Rtmpq11Eub/file2cc6356910d4_restore.nii.gz' to '/tmp/Rtmpq11Eub/file2cc6356910d4.nii.gz', reason 'No such file or directory'Error in oro.nifti::readNIfTI(..., reorient = reorient) : 
  File(s) not found!

So I googled a lot and come here,BUT there is something different between my situation and #issue10 posted on home page:
1.There is no folder called fsl under \user\lib in my enviroment.I just followed the instruction of the official website when I install FSL .
2. It seems that I didn't install FSL correctky.From the link:https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux,I passed the first check installation echo $FSLDIR and returns /usr/local/fsl,BUT it failed on the second check flirt -version,it returns flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory .HOWEVER,I can still open the GUI of FSL .I don't know what I am supposed to do.

fslr experts and devlopers:

I encountered an error when I ran an R code on Rstudio on Xubuntu 18.04 LTS VirtualBox on Windows 10 host.

There was no issue with the Installation of {fslr} and {ATNsR}. I installed fsl v.5 using Neurodebian.

As you suggested I included the "export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" in my .profile file on my linux VM. This did not clear the error and it remains.

DSC.Coef = try(fsl_dice(img_1,img_2))
fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
fslstats: 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 system(cmd, intern = intern) : error in running command
2: In system(cmd, intern = intern) : error in running command

If you have any remedy or suggestions for this error, it would be greatly appreciated.

Thank you.
SC

After some trouble with packrat and updating fslr I am getting the following error, when I try to open a nifit from within R:

library(fslr)
ld = Sys.getenv("LD_LIBRARY_PATH")
Sys.setenv("LD_LIBRARY_PATH"=paste0(ld, ":/usr/lib/fsl/5.0"))
mni <-  readNIfTI("data/Input/mni.nii.gz",
                  reorient = FALSE)
> fslr::fslview(mni)
FSLDIR='/usr/share/fsl/5.0'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; sh "${FSLDIR}/etc/fslconf/fsl.sh"; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslview '/tmp/Rtmpc9D8No/file126f73c02102.nii.gz' 

sh: 1: /usr/share/fsl/5.0/bin/fslview: not found
Error in system(cmd, intern = intern) : error in running command
In addition: Warning messages:
1: In get.fsl() : Setting fsl.path to /usr/share/fsl/5.0
2: In get.fsloutput() : Can't find FSLOUTPUTTYPE, setting to NIFTI_GZ

Here my (local) .bash_profile:

. ~/.profile
. ~/.bashrc

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/fsl/5.0

And the last lines of my (local) .bash_rc

# fslr tipp, 01.03.17
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/fsl/5.0 in your .bashrc

# from terminal man fsl
 . /etc/fsl/5.0/fsl.sh

## bash
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

My Ubuntu version is: 16.04.2 LTS (Xenial Xerus)
R version: 3.3.4
fslr version: 2.13.1 (but I get the same error, when using the cran version).

Any ideas?

fslr has been installed on my ubuntu system as follows. BTW, I got have.fsl() = FALSE,
Anybody knows why?

I need to solve this issue. Please.
OS : Ubuntu 18.04.
HW: Thinkpad T430 (Laptop)

> devtools::install_github("muschellij2/fslr")
Downloading GitHub repo muschellij2/fslr@master
These packages have more recent versions available.
Which would you like to update?

1: All                                              
2: CRAN packages only                               
3: None                                             
4: neurobase (72992281f... -> dc146c2a5...) [GitHub]
5: RNifti    (0.11.0       -> 0.11.1      ) [CRAN]  

Enter one or more numbers, or an empty line to skip updates:
2
RNifti (0.11.0 -> 0.11.1) [CRAN]
Installing 1 packages: RNifti
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
URL 'https://cloud.r-project.org/src/contrib/RNifti_0.11.1.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 646195 bytes (631 KB)
==================================================
downloaded 631 KB

* installing *source* package ‘RNifti’ ...
** 패키지 ‘RNifti’는 성공적으로 압축해제되었고, MD5 sums 이 확인되었습니다
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c main.cpp -o main.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/adler32.c -o zlib/adler32.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/compress.c -o zlib/compress.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/crc32.c -o zlib/crc32.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/deflate.c -o zlib/deflate.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/gzclose.c -o zlib/gzclose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/gzlib.c -o zlib/gzlib.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/gzread.c -o zlib/gzread.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/gzwrite.c -o zlib/gzwrite.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/infback.c -o zlib/infback.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/inffast.c -o zlib/inffast.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/inflate.c -o zlib/inflate.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/inftrees.c -o zlib/inftrees.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/trees.c -o zlib/trees.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/uncompr.c -o zlib/uncompr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zlib/zutil.c -o zlib/zutil.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c znzlib/znzlib.c -o znzlib/znzlib.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c niftilib/nifti1_io.c -o niftilib/nifti1_io.o
niftilib/nifti1_io.c: In function ‘nifti_disp_lib_version’:
niftilib/nifti1_io.c:465:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
    Rc_printf("%s, compiled %s\n", gni_version, __DATE__);
                                                ^~~~~~~~
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNifti.so main.o zlib/adler32.o zlib/compress.o zlib/crc32.o zlib/deflate.o zlib/gzclose.o zlib/gzlib.o zlib/gzread.o zlib/gzwrite.o zlib/infback.o zlib/inffast.o zlib/inflate.o zlib/inftrees.o zlib/trees.o zlib/uncompr.o zlib/zutil.o znzlib/znzlib.o niftilib/nifti1_io.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-RNifti/00new/RNifti/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RNifti)

The downloaded source packages are in
        ‘/tmp/RtmpoHmLj4/downloaded_packages’
✔  checking for file ‘/tmp/RtmpoHmLj4/remotes248d8ce741b/muschellij2-fslr-3cf1909/DESCRIPTION’ ...
─  preparing ‘fslr’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘fslr_2.24.1.tar.gz’
   
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘fslr’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fslr)
> library(fslr)
필요한 패키지를 로딩중입니다: oro.nifti
oro.nifti 0.10.1
필요한 패키지를 로딩중입니다: neurobase
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Please cite the fslr package using:
Jenkinson M, Beckmann CF, Behrens TE, Woolrich MW, Smith SM (2012).
“FSL.” _Neuroimage_, *62*(2), 782-790.

Muschelli J, Sweeney E, Lindquist M, Crainiceanu C (2015). “fslr:
Connecting the FSL Software with R.” _The R Journal_, *7*(1), 163-175.
> have.fsl()
[1] FALSE

@muschellij2 Please look at this issue.

Hi. Love this package, it's been really nice to grab data straight into R for further use.

Would you consider making a wrapper for cluster too? Would be beneficial for tables etc.

Just a suggestion, keep up the good work!

Thanks John,

Continue to the last question, I have a nifti file in the end. Great! I checked the path /usr/bin which has all just fsl symlinks in the format of fsl5.0-aff2rigid, and the path /usr/share/fsl/5.0 has folders as:

~$ cd /usr/share/fsl/5.0/
5.0$ ls
bin data doc etc tcl
5.0$ ls -l
total 20
lrwxrwxrwx 1 root root 20 Aug 24 2013 bin -> ../../../lib/fsl/5.0
lrwxrwxrwx 1 root root 7 Aug 24 2013 data -> ../data
drwxr-xr-x 6 root root 4096 Oct 22 23:02 doc
drwxr-xr-x 8 root root 4096 Oct 22 23:02 etc
drwxr-xr-x 3 root root 12288 Oct 22 23:02 tcl

Now I have two more questions (unrelated to the above):

1. Does fslr package have function like fslroi? Or could I perform this in other ways?

2. If I have a nifti file in dims of 170 x 240 x 240, could I use fslr package to pad it into a cubic file in dims of 240 x 240 x 240? Or do you know if there are other ways to do this?

Great thank,
Kaiming

Dear all,

my issue is similar to #2.

# fslr works
> library("fslr")
Loading required package: oro.nifti
oro.nifti 0.7.2
Loading required package: neurobase
> volume.t2 <- readNIfTI("data/Neurohacking_data-0.0/BRAINIX/NIfTI/T2.nii.gz",
+                        reorient = FALSE)
> getOption("fsl.path")
NULL
> fslr::dim_(volume.t2)
[1]   3 512 512  22   1   1   1   1

# but when calling fslstats, which invokes libnewimage.so, I get an error:
> fslstats(volume.t2, opts = "-m")
FSLDIR='/usr/share/fsl/5.0'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; sh "${FSLDIR}/etc/fslconf/fsl.sh"; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslstats  "/tmp/Rtmp8FGRWx/file8e5f71acb2.nii.gz" -m

/usr/share/fsl/5.0/bin/fslstats: 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/share/fsl/5.0
2: In get.fsloutput() : Can't find FSLOUTPUTTYPE, setting to NIFTI_GZ

# Also some trials to change the fsl.path option didn't solve this
> options(fsl.path="/usr/lib/fsl/5.0")
> fslstats(volume.t2)
FSLDIR='/usr/lib/fsl/5.0'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslstats  "/tmp/Rtmp8FGRWx/file8e5745e6178.nii.gz" 

sh: 1: /usr/lib/fsl/5.0/bin/fslstats: not found
Error in system(cmd, intern = TRUE) : error in running command

# Also other commands behave this way:
> flirt.help()
sh: 1: usr/local/fsl/bin/flirt: not found
Error in system(cmd, intern = TRUE) : error in running command

# and another trial to set the path
> options(fsl.path="/usr/share/fsl/5.0")
> fslstats(volume.t2)
FSLDIR='/usr/share/fsl/5.0'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; sh "${FSLDIR}/etc/fslconf/fsl.sh"; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslstats  "/tmp/Rtmp8FGRWx/file8e54fb3a214.nii.gz" 

/usr/share/fsl/5.0/bin/fslstats: 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

However from the terminal fslstats just works:

$ fslstats T2.nii.gz -m

My feeling is that it is something with the Path in ubuntu (I am on 16.04) and/or the file.path option in R and maybe the automatic add_bin in get.fsl() which is called by fslr::fslstats.

To .bashrc I added:

. /etc/fsl/5.0/fsl.sh

And in .profile I added to the PATH:

/usr/lib/fsl/5.0

I would be happy about any advice.

Thanks,
Malte

1. function topup is currently (version 2.20.3) not in NAMESPACE
2. fslr:::topup("file.nii", "param.txt", out="outfile")

creates call ( non existent option infile )

topup --infile=file.nii --datain=param.txt --out=out --warpres=10 --subsamp=1 --fwhm=8 --miter=5 --ssqlambda=1 --regmod=bending_energy --estmov=1 --minmet=0 --splineorder=3 --numprec=double --interp=spline --scale=0 --regrid=0 --verbose

instead of ( correct option imain )

topup --imain=file.nii --datain=param.txt --out=out --warpres=10 --subsamp=1 --fwhm=8 --miter=5 --ssqlambda=1 --regmod=bending_energy --estmov=1 --minmet=0 --splineorder=3 --numprec=double --interp=spline --scale=0 --regrid=0 --verbose

Regards,

Joerg

Hi! The arch AUR installed the fsl into /opt/fsl which is differ from the default /usr/local/fsl and fsl cannot be automatically accessed. After adding . ${FSLDIR}/etc/fslconf/fsl.sh
into .Renviron, it shows $FSLOUTPUTTYPE not setted. My zsh shell can run fsl normally. Thanks!

Hi John,

Thanks for all your work on this software. I have a brain image series and a corresponding binary segmentation image. I understand that fslreorient2std is a basic operation applied to images to standardize the orientation. How can I apply this to the corresponding binary segmentation image? I see that the function allows to write the transformation matrix as output. How do I use this to transform the segmentation map as well?

Thanks for your help!

I am working on a Mac with R version 3.2.1 (not through a virtual machine, directly with the Mac) and am trying to install fslr. I have entered the following commands:

if(!require(devtools)){install.packages('devtools')}
devtools::install_github("muschellij2/fslr")

and received the following output related to the second command:

Downloading GitHub repo muschellij2/fslr@master
from URL https://api.github.com/repos/muschellij2/fslr/zipball/master
Installing fslr
trying URL 'http://cran.cnr.berkeley.edu/bin/macosx/contrib/3.2/matrixStats_0.50.2'
Content type 'application/x-gzip' length 846649 bytes (826 KB)
'=================================================='
Error: Don't know how to decompress files with extension 50.2

When I looked into the error, it appears that something is chopping off the end of the filename through the CRAN mirror (the filename should be matrixStats_0.50.2.tgz). Any help on why this is occurring?

Hi John,

I am a neuroimaging researcher trying to process DSC MRI data.

I have thus far used Verbena for this that is available in the latest version of FSL although there are some issues with the output. The CBV file that it outputs appears to be normalised to an unknown entity with singular value decomposition.

My question is therefore twofold:

1. Is there going to be implementation into FSL-R of Verbena?
2. Are there any other good options for its analysis to produce rCBV files in the framework of R?

Is there a good way to load multiple NIFTI files that are already stored in environment variables into the fsleyes plugin (within R)?

A rather cumbersome solution I am using at the moment is to run a different fsl function and copy paths of individual files into the opts = "" part of the code.
This does not work if I use the tempdir path...so I am assuming it requires NIFTI inputs.

I've been getting some OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable errors from FSL, along with OpenBLAS blas_thread_init: RLIMIT_NPROC XXXX current, XXXX max.

I've fixed this by setting

export OMP_NUM_THREADS=1

in my ~/.bash_profile as per OpenMathLib/OpenBLAS#888, but again maybe an ugly workaround and I'm unsure of the exact problem. Just FYI to users.

Hi there,

Is there a way to use FSL's inverse warp feature? I can run FNIRT fine but would like to apply the inverse warp feature without having to use terminal

Thank you

Hi everyone,

I want to use the function mid_sagittal_align in R. I already have installed FSL5.0, R, R studio, fslr, etc...
So, when I use it, it gives me the next error:

FSLDIR='/usr/share/fsl/5.0'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; sh "${FSLDIR}/etc/fslconf/fsl.sh"; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslhd "/tmp/Rtmpveqwpe/file14d614372173.nii.gz"
/usr/share/fsl/5.0/bin/fslhd: error while loading shared libraries: libfslio.so: cannot open shared object file: No such file or directory
Error in system(cmd, intern = TRUE) : error in running command

I checked to have the fslhs and libfslio.so files
I am using Ubuntu 16.10
Does anyone knows what could be the problem?

Thanks in advance.

Dear all,

I´m new to linux and coding in general and any help will be appreciated. I download a VMware and I am running FSL now but I am unable to process SIENA. I already tried config a shared folder with Win10 via mng folder and also tried to process from a USB (ExFat format, I already installed the drive and the usb is read without issues) but the same error keeps appearing once a try to process siena:

[fsluser@localhost NMDA]$ siena avendano2.nii avendano1.nii
/usr/local/fsl/bin/bet2: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/bet2: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/flirt: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/flirt: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
/usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
/usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: dc: register 'd' (0144) is empty
dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: register 'e' (0145) is empty
dc: dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: dc: input base must be a number between 2 and 16 (inclusive)
dc: dc: dc: dc: register 'd' (0144) is empty
dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: register 'e' (0145) is empty
dc: dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: register 'i' (0151) is empty
dc: dc: dc: dc: dc: dc: dc: register 'd' (0144) is empty
dc: output base must be a number greater than 1
dc: dc: input base must be a number between 2 and 16 (inclusive)
dc: output base must be a number greater than 1
dc: stack empty
dc: dc: dc: register 'e' (0145) is empty
dc: dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: dc: input base must be a number between 2 and 16 (inclusive)
dc: dc: dc: dc: register 'd' (0144) is empty
dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: register 'e' (0145) is empty
dc: dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: register 'i' (0151) is empty
dc: dc: dc: dc: dc: /usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: stack empty
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/pngappend: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/bin/rm: cannot remove 'grA_halfwayto_B?.???': No such file or directory

Finished. The SIENA report can be viewed by pointing your web browser at:
file:/home/fsluser/Desktop/NMDA/avendano2_to_avendano1_siena/report.html
Estimated percentage brain volume change (PBVC) =

Dear John,

I was trying to run fslmaths input output -odt short in fslr R package, as below:

fslmaths("data.img", opts = "-odt short") # data.img could be NIFTI or ANALYZE

FSLDIR='/usr'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; FSLOUTPUTTYPE=NIFTI; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fsl5.0-fslmaths "/home/kaimingyin/Desktop/data.img" -odt short "/tmp/RtmpceSI2O/file2244322574e3";

Error in command line: unknown option "-odt"

It reports error as above, do you know how to fix it?

Also, should I run the ourput in one of the below ways like:

output <- fslmaths("data.img", opts = "-odt short")
or
fslmaths("data.img", outfile = "output.img", opts = "-odt short")

Thanks,
Kaiming

I have just installed FSL. It works fine from the terminal as well as the GUI. After I installed fslr I tested it by using the the fsl_biascorrect() function. Here is what I get back:

sh: 1: /usr/lib/fsl/5.0/bin/fast: not found
Error in oro.nifti::readNIfTI(..., reorient = reorient) : 
  File(s) not found!
In addition: Warning messages:
1: In file.remove(seg_file) :
  cannot remove file '/tmp/RtmpYkUvUs/file23d532a6435b_seg.nii.gz', reason 'No such file or directory'
2: In file.rename(output, outfile) :
  cannot rename file '/tmp/RtmpYkUvUs/file23d532a6435b_restore.nii.gz' to '/tmp/RtmpYkUvUs/file23d532a6435b.nii.gz', reason 'No such file or directory'

I believe I have set up the path and install correctly but I can go over what I did if necessary. have.fsl() returns TRUE.

The issue seems to be, I think, that fast and other relevant files are actually in /usr/lib/fsl/5.0/. There is no /bin folder at all. I am not sure why this is. I simply installed FSL via: sudo apt-get install fsl-5.0-complete. From what I can tell from the fslr command output to shell, fslr adds the /bin to the path automatically: ${FSLDIR}/bin/fast.

Do you think I have installed FSL incorrectly?

R studio is kicking the error below when I try to run this code:

# Commented out as all packages are installed now
install.packages("flexdashboard")
install.packages("rmarkdown")
install.packages("knitr")
install.packages("readxl")
install.packages("oro.dicom")
# Install package "devtools" which is used to install package "neurobase" and "fslr"
install.packages("devtools")
# Install neurobase
devtools::install_github("muschellij2/neurobase")
# Install fslr
devtools::install_github("muschellij2/fslr")

# Loading all libraries
library(flexdashboard)
library(rmarkdown)
library(knitr)
library(readxl)
# Load required library to read multiple DICOM files
library(oro.dicom)
library(devtools)
# Load the neurobase and fslr
library(neurobase)
library(fslr)

options(fsl.path="/Library/Frameworks/R.framework/Versions/4.1/Resources/library/fslr")

if (have.fsl()){
  system.time({
    dims = c(50, 50, 20)
    x = array(rnorm(prod(dims)), dim = dims)
    img = nifti(x, dim= dims, 
                datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
                cal.max = max(x), pixdim = rep(1, 4))
    s.img = fslsmooth(img, retimg=TRUE)
  })
}

Error:

FSLDIR='/Library/Frameworks/R.framework/Versions/4.1/Resources/library/fslr'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslmaths "/private/var/folders/1f/n1lfmhwx41gcpl_9k02ln2cr0000gn/T/RtmpMYGT6a/filee3ac73f6c7d1.nii.gz" -s 10 "/var/folders/1f/n1lfmhwx41gcpl_9k02ln2cr0000gn/T//RtmpMYGT6a/filee3ac4eb8a5d1";

rest/of/path/library/fslr/bin/fslmaths: No such file or directory
Error in oro.nifti::readNIfTI(..., reorient = reorient) :
File(s) not found!

Any idea why this might be? I'm lost with it right now.

Dear guys,

I'm using fslr package with FSL 5.0 installed in Ubuntu. I have set up the path successfully as:

library(fslr)
options(fsl.path='/usr/share/fsl/5.0')
options(fsl.outputtype = 'NIFTI')

However, when I call flirt.help(), I get an error message:

usr/share/fsl/5.0/bin/flirt: 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

The similar error also happens when I call fslbet.help(), as:

/usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory
Error in system(cmd, intern = TRUE) : error in running command

Could you help me?

Thanks,
Kaiming

Hello,
I want to convert the 3d 111 flair image of the same patient to 3d 115 flair. And I want it to be in the transversal plane. I opened applyxfm in the user interface in fsl.

I put the flair image of the patient with the voxel sizes I wanted as the reference volume. It only takes the patient's voxel dimensions, not the image content, am i right? If the image will register, it will be wrong..

And I clicked the identity matrix button as transformation matrix question.
Is there anything wrong with all this? Please let me know.

By the way, i ran this command and it didnt work.
flirt -in /ms/flairhigh.nii -ref /ms/flairhigh.nii -applyxfm -out /ms/out

The image came in sagittal, but the transverse plane I put in was (user interface option)
Thanks in advance!

Hi John,
I want to use probtrackx. However, rstudio suggests that could not find function "probtrackx". Other functions in fslr work well. I can also run probtrackx in ubuntu.

Can you help me solve this problem? Thanks
Li

From an email:
"I seem to have some trouble understanding how to change values for parameters ‘g’ and ‘f’ in the fslbet function. I have been looking for examples of R commands using it but can’t seem to find any."

The opts argument is where you can change these:

fslbet(infile, opts = "-f 0.1 -g 0.2")

I am trying to use the fslsmooth function on a NIFTI object. It is returning the following error:

Error in gzfile(paste(filename, "nii.gz", sep = "."), "wb", compression = compression) :
cannot open the connection

I am having a difficult time understanding what is causing this error, or how to fix it. I have verified that the input objects are valid NIFTI objects. Here is a screenshot that shows the summary of each NIFTI object as well as the syntax of the fslsmooth function call.

Any idea where to look as to how to resolve this? This same code chunk has previously worked for me on the same NIFTI files, so I'm at a bit of a loss as to why suddenly it is unable to execute.

Dear John,

Could function fslreorient2std() has both the input_image and output_image? It seems now fslreorient2std() only accept one file as the input.

fslreorient2std.help()
Usage: fslreorient2std <input_image> [output_image] fslreorient2std is a tool for reorienting the image to match theapproximate orientation of the standard template images (MNI152).It only applies 0, 90, 180 or 270 degree rotations.It is not a registration tool.It requires NIfTI images with valid orientation informationin them (seen by valid labels in FSLView). This toolassumes the labels are correct - if not, fix that before using this.If the output name is not specified the equivalent transformation matrix is written to the standard output

fslreorient2std()
Error in checkimg(file, ...) :
argument "file" is missing, with no default

Thanks,
Kaiming

eddy has been replaced by eddy_openmp and eddy_cuda in fsl. This requires a chaange of the call
in function eddy ...

From the fsl/eddy manual:

The eddy executables

eddy is a very computationally intense application, so in order to speed things up it has been parallelised. This has been done in two ways, resulting in two different executables

eddy_openmp: This executable has been parallelised through OpenMP, which allows eddy to use more than one core/CPU when running.

eddy_cuda: The other executable has been parallelised with CUDA, which allows eddy to use an Nvidia GPU if one is available on the system. 

Hence, there is not longer an executable named eddy and when I refer to the eddy-command in the rest of this users guide it is implied that this is either eddy_openmp or eddy_cuda. The eddy_cuda version is potentially much faster than eddy_openmp and not all new features will be available for the OpenMP version. This is because the slow speed makes it almost impossible to test the more time-consuming options thoroughly.