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Hi Taylor,

Thanks for asking.  Yes, I was performing the installation with sudo.

I have since followed a suggestion to download the missing tools from https://nifti.nimh.nih.gov/pub/dist/src/fsliolib.  I placed them within the fsl-6/fslpython/envs/fslpython/bin directory as this is where the soft links expected them to be, and now we seem to be in business.

Thank you —
Amanda

On Jun 19, 2019, at 12:30 AM, Taylor Hanayik <[log in to unmask]<mailto:[log in to unmask]>> wrote:

Hi Amanda,

Have you tried removing the fslpython directory and installing fslpython with sudo?



Cheers,

Taylor Hanayik


Taylor Hanayik PhD
Analysis Research Software Engineer
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]<mailto:[log in to unmask]>





On 18 Jun 2019, at 21:49, Grethe, Amanda <[log in to unmask]<mailto:[log in to unmask]>> wrote:

Hello all —

I am trying to install FSL 6.0.1 and am running into some problems. We are using ubuntu 14.04 LTS with python 2.7.6.

I seem to be unable to install the im* commands (imcp, immv, imglob).  I have tried advice to remove the fslpython directory and reinstall using fslpython_install.sh.

The installer seems to run through correctly, with stage 2 taking several minutes.  Upon completion there are no error messages, and there is no log file within /tmp.

I can see that the soft links for the im* commands exist in the fsl bin directory:

cbt-imaging@CBT-Imaging:/usr/local/fsl-6$ ll /usr/local/fsl-6/bin/imcp
lrwxrwxrwx 1 root root 50 Jun 12 11:42 /usr/local/fsl-6/bin/imcp -> /usr/local/fsl-6/fslpython/envs/fslpython/bin/imcp

However, the commands do not appear to exist within fslpython/bin:
cbt-imaging@CBT-Imaging:/usr/local/fsl-6$ ls /usr/local/fsl-6/fslpython/envs/fslpython/bin/i*
/usr/local/fsl-6/fslpython/envs/fslpython/bin/icu-config
/usr/local/fsl-6/fslpython/envs/fslpython/bin/icuinfo
/usr/local/fsl-6/fslpython/envs/fslpython/bin/idle3
/usr/local/fsl-6/fslpython/envs/fslpython/bin/idle3.5
/usr/local/fsl-6/fslpython/envs/fslpython/bin/ipython
/usr/local/fsl-6/fslpython/envs/fslpython/bin/ipython3

I modifed fslpython_install.sh so it would not delete the log file at the end, deleted the fslpython directory, and reran the installer.  I reviewed the log file and cannot find any errors, only a warning regarding pip not being listed as a conda dependency.

Are there any other suggestions as to how to resolve this?

Thank you —
Amanda



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