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/usr/lib/fsl/5.0/bin/fast: not found #11
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Please see my comment in #10 |
I used your script to create a |
Can you be more explicit? Code + MWE required. |
Here is the code I am running from my working directory. Note that I have removed the path name for privacy purposes.
To check that the directory indeed contains the files:
Session info:
Let me know if you need anything else. |
libnewimage.so should not be in the bin directory. Can you copy libnewimage (and all other lib files) to the John |
What Linux distro are you on? May be relevant: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;534aeecf.1606 Can you run |
What is your $LD_LIBRARY_PATH ? |
Ubuntu 16.04.2 LTS
No... I get the following error:
Running
|
Maybe try: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux#Debian.2FUbuntu_users. I'm not sure zsh is supported by default: https://gist.github.com/methou/eab939aae92238fea48e Have you tried I would test the neurodeb distro to make sure that works. If it does, you may simply want to symlink those over. |
I am really new to all this to be honest so I'm not really sure what I'm doing.
Sorry, this isn't really an fslr problem but I appreciate you trying to help me. |
Please read: https://stackoverflow.com/help/mcve for help making a MWE.
I don't understand what you mean by "If I run it, it works fine." If the
script fully runs (can you provide an example image), please post the
script and output. Try to run the same thing in fslr and show the error.
Please also ls your /usr/local/fsl/bin and /usr/local/fsl/lib/
Thanks
John
John
…On Thu, Aug 31, 2017 at 11:25 AM, snamjoshi ***@***.***> wrote:
I am really new to all this to be honest so I'm not really sure what I'm
doing.
fsl5.0 is located in /usr/bin/fsl5.0-fast. If I run it, it works fine. I
did the symlink and now echo $LD_LIBRARY_PATH returns /usr/lib/fsl/5.0 (
/5.0 is now linked to /usr/share/fsl but this may not have been what you
meant). I'm not really sure what the proper usage of the library path
variable is so I'm trying to read up on that before I break anything
further. I'm thinking about removing everything and just starting over at
this point.
Sorry, this isn't really an fslr problem but I appreciate you trying to
help me.
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I'm not sure what other code/script I can provide you to reproduce my problem. Part of the issue is I am not exactly sure what will be useful for you because I am not sure how to fix the problem I am having. I can give you my directory structure relevant to
I misunderstood what you were asking above. I was indicating that I have linked |
Have you tried fast.help?
On Thu, Aug 31, 2017 at 11:53 AM snamjoshi ***@***.***> wrote:
I'm not sure what other code/script I can provide you to reproduce my
problem. Part of the issue is I am not exactly sure what will be useful for
you because I am not sure how to fix the problem I am having. I can give
you my directory structure relevant to fsl if that would help.
I misunderstood what you were asking above. I was indicating that
fsl5.0-fast is able to run when evoked from the terminal.
I have linked /usr/local/fsl/bin and /usr/local/fsl/lib. From the
terminal, running /usr/local/fsl/bin/fast starts the program. The
parameters/optional commands come up on the screen. It does not give an
error about shared libraries. I then restarted R and with options(fsl.path
= "/usr/local/fsl"), I get the exact same error I listed in the post
above where I gave my R code: /usr/local/fsl/bin/fast: error while
loading shared libraries: libnewimage.so: cannot open shared object file:
No such file or directory
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John
|
Do you mean the man page for fast? There isn't one... there is a man page for fsl and I have learned the following:
Neither of these provide new information for me. I purged fsl-5.0-complete from my system, including from
Note that, by default installation, the lib files are in
You originally pointed me in the direction of an earlier post with the following script. I have not yet run it yet in the MWE.
It seems that you are copying everything from Does this constitute an MWE you can work with? Is there anything else I can add? |
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 thefsl_biascorrect()
function. Here is what I get back: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?
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