I also just encountered this problem when running the fslinstaller.py on a the distributed VM running on a Windows host. The download always fails at 99% but only when using the fslinstaller.py script. wget works fine.
Did anyone ever figure out the cause? In any case, here's a work around.
wget -c http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
wget -c http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.2-centos6_64.tar.gz
wget -c http://fsl.fmrib.ox.ac.uk/fsldownloads/md5sums/fsl-5.0.2-centos6_64.tar.gz.md5
./fslinstaller.py -f fsl-5.0.2-centos6_64.tar.gz -C `cat fsl-5.0.2-centos6_64.tar.gz.md5` -d /usr/local/
> When trying to install FSL v5 on a Windows system using VMWare Player (python fslinstaller script, as suggested in the online
> instructions) downloading seems to proceed for several minutes, then I get the following message:
>
> Downloading FSL version 5.0.1
> 1521614848/1521628308 - 99%[FAILED] Failed to download file.
>
> If I try to install as root user (su -c "python fslinstaller.py")(+/- specifying destination directory with the -d option), or with
> manual installation (python fslinstaller -o) I get the same message - failed at 99%download.
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