Problems installing FSL

Software Support
84

Hi Paul,

Thanks a lot for the quick response!

Increasing memory worked for the installation of 6.0.6. And by using the miniconda for python 3.11, I was also able to install 6.0.7:

python3 fslinstaller.py -V 6.0.7 -d /packages/apps/fsl/6.0.7 --miniconda https://repo.anaconda.com/miniconda/Miniconda3-py311_24.4.0-0-Linux-x86_64.sh

Thank you for all the help!

Regards,
Nil

85

Hello @paulmccarthy

I want to install fsl on an HPC and I am running to the same error as everyone which is:

ERROR occurred during installation!

This command returned an error: /usr3/graduate/mary79/fsl/bin/conda env update -p /usr3/graduate/mary79/fsl -f fsl-6.0.7.12_linux-64.yml

I tried these commands and none of them worked:

  1. python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    logfile
  2. CONDA_AUTO_UPDATE_CONDA=false python ./fslinstaller.py.logfile

Can you help me with this issue?
I am runnning on a virtual environment and I am using Python 3.6.12

Blockquote

86

Hi @maryam.riazi, have you checked the contents of the log file?

87

Hi @paulmccarthy
I have attached the log file of each command in my comment.
I looked at them but unfortunately, I could not figure out what is the problem.
My guess is that it is something related to version problem.
fsl has already been installed on the HPC and maybe the error is because I am trying to intsall it on a virtual enivronment.
How can I specify another directory for fsl installation destination?

88

Hi @maryam.riazi, sorry - I didnā€™t notice the log file links. The first logfile implies that you passed an invalid URL to the --minconda option. The second logfile implies that you have run out of disk space. FSL requires about 10GB of free disk space, so yo need to make sure that you have enough space available. You can install FSL to a different locaion with the -d option, e.g.:

python fslinstaller.py -d /path/to/some/other/location
89

Thanks @paulmccarthy
I specified another location and it worked!

1 Like
90

Hey, hope you are doing well.

My computer be able to install first 2 step ( downloading and installing miniconda) but couldnā€™t do last step: Installing FSL. It doesnā€™t even start. I am adding log file as linklog file. If you can help, I would be very happy. Thank you in advance.

Btw, I am using Mac Sonoma 14.3.1

91

Hi @Rufeyda_Yagci, could you try running the installer script like this?

export SYSTEM_VERSION_COMPAT=0
python fslinstaller.py

On certain macOS installations, the version of macOS is being incorrectly detected. I will add a work-around into the installer script so that this shouldnā€™t happen in the future.

92

It worked! Thank you so much :slight_smile:

1 Like
93

Hi @paulmccarthy

During the installation of FSL, I received an error message like the one below.

ERROR occurred during installation!

This command returned an error: /Users/lim.seokbeen/fsl/bin/conda env update -p /Users/lim.seokbeen/fsl -f fsl-6.0.7.13_macos-M1.yml

I confirmed my .log file and follow the instructions of this page, however, I can not install FSLā€¦
Could you please give me your advice to install FSL software?

I attached my log below.
Log Link

94

Hi @seokblim, Iā€™m not sure why the installation is failing for you, but you could try a few things:

  • Clear the DYLD_LIBRARY_PATH variable in your shell environment (I donā€™t think this is the cause, but it can sometimes have an affect)
  • Use a newer version of miniconda
  • Use the system Python installation instead of a homebrew installation

You can do all of these with the following commands:

unset DYLD_LIBRARY_PATH
/usr/bin/python3 fslinstaller.py --skip_ssl_verify --miniconda https://repo.anaconda.com/miniconda/Miniconda3-py311_24.5.0-0-MacOSX-arm64.sh
95

Hi @paulmccarthy

Thank you for your warm support and for giving me great advice.
Although Itā€™s not worked for me, you gave me a clue to try to install it another way.
It might be another issue with my computer.

Thanks again!

96

Hi @seokblim, it could also be your network connection - are you working from within (for example) a corporate or hospital network? Do you have the option of trying the installation from a different internet connection?

97

Hello @paulmccarthy

Thank you for your other suggestion!
Yes, I am working in a hospital, and Typically, I use a hospital network.
What I asked you about before is the situation in which I tried to install FSL on my houseā€™s internet connection.
However, Today, I tried to install the FSL using the command that you suggested the clue in the hospital network.
As per your suggestion, It might be a network issue; I will try to install it when I go back to my house.

Thatā€™s a really good point; thank you for your support!!

98

hi @paulmccarthy
I have read through most of the discussions in the forum and noticed that many users, including myself, are encountering issues during the ā€œInstalling FSL into /home/[user]/fslā€¦ā€ section. While your suggestions have been incredibly helpful, I would like to propose an idea that could benefit a large number of users.
Given the frequent connectivity issues during the download process, would it be possible for your team to provide a repository where all necessary files and packages can be downloaded manually? This would allow the installation process to proceed from a local repository, thereby minimizing the reliance on unstable internet connections.
Thank you for considering this requestā€¦

99

Hi @SoheilZ, this is already possible, but we have not yet written instructions on how to do it. All of the packages that comprise a FSL installation are downloaded from an Oxford-based conda channel and from conda-forge. It is possible to tell the fslinstaller script to download packages from an alternative conda channel with the --channel option. So you could set up your own local conda channel containing the larger packages, and direct the fslinstaller script to download the packages from there.

100

Hi @paulmccarthy

I am trying to install the FSL on the HPC at my institute (the University of Arizona), but I wasnā€™t able to get past the installation of Miniconda. Would you mind suggesting some fixes?

My log is attached: Log

Thank you!

101

Hi @Diheng_Zhang, could you try running the installer with the --throttle_downloads option? e.g.:

python fslinstaller.py --throttle_downloads
102

Hi @paulmccarthy Thank you so much for your prompt response. I tried it but it seems to get to the same error.

Here is the Log.

103

Hi @Diheng_Zhang, would you be able to try running the miniconda installer directly? You can do this by running the following commands:

wget https://repo.anaconda.com/miniconda/Miniconda3-py311_24.3.0-0-Linux-x86_64.sh
sh ./Miniconda3-py311_24.3.0-0-Linux-x86_64.sh -b -p ./miniconda

If this produces the same error, then you may need to get in touch with your IT administrator - perhaps they have configured your system to restrict what can be done with conda.