Problems installing FSL

paulmccarthy · June 7, 2024, 8:33am

Can you share the output that was printed, and ideally a copy of the log file?

anne.a · June 7, 2024, 3:32pm

Hi @paulmccarthy, I suspected that was the problem, but my lack of experience makes log files difficult to interpret.

I followed your instructions and it worked like a charm, thank you!

cchunharas · June 14, 2024, 12:18am

I ran python ~/Downloads/fslinstaller.py from the command line on a Macbookpro M3 with Sonoma 14.4 and got stuck at step 3 (Installing FSL into /Users/xxxx/fsl). I have installed fsl on multiple machines earlier but never ran into something like this before.

I tried almost all of the solutions posted here but they did not work. Here is my log file.
Could you please kindly suggest?
Highly appreciated!

Chaipat
fsl_installation_20240614011923.txt (19.2 KB)

paulmccarthy · June 14, 2024, 9:51am

Hi @cchunharas, this looks like an issue with your network connection - one of the downloads seems to have been interrupted. Could you try running the installer like this, to try and make the downloads more resilient? You should not need to use the --miniconda option:

python fslinstaller.py --throttle_downloads

cchunharas · June 16, 2024, 1:22pm

Problem has been solved. Thank you again @paulmccarthy

Nil · June 17, 2024, 11:23pm

Hello @paulmccarthy,

I’m also having the similar issues with installing FSL recently. It would be very helpful if you could help me troubleshoot with the errors.

I’m trying to install FSL on a linux cluster, and the OS is Rocky 8.9. Here are the commands I tried:

Used the python3 from /usr/bin/python

a. Command used: python fslinstaller.py -V 6.0.6 -n
Error log
Built an empty environment called “fsl_base”, with mamba, and python 3.11. So the python was from /packages/envs/fsl_base/bin/python.

a. Command used: python fslinstaller.py -V 6.0.6 -n
Error log

b. Command used: CONDA_AUTO_UPDATE_CONDA=false python ./fslinstaller.py -V 6.0.6 -n
Error log

c. Command used: python fslinstaller.py --throttle_downloads
Error log

Thanks in advance!
Nil

paulmccarthy · June 18, 2024, 9:41am

Hi @Nil, if you are trying to install FSL 6.0.6, can you try running the fslinstaller.py script specifying an alternative Python 3.10-based miniconda installer, e.g.:

python fslinstaller.py -V 6.0.6 -d /packages/apps/fsl/6.0.6 --miniconda https://repo.anaconda.com/miniconda/Miniconda3-py310_24.4.0-0-Linux-x86_64.sh

We are updating the release system so that an appropriate miniconda will be automatically selected (and will probably eventually switch to micromamba), so this shouldn’t be necessary in the future.

Nil · June 18, 2024, 3:23pm

Hi Paul @paulmccarthy,

Thanks for your quick response!

When running the command you suggested in a mamba (1.5.1) made environment with python=3.10.14, I got a similar conda update error:
08:11:30 fslinstaller.py:3209: This command returned an error: /packages/apps/fsl/6.0.6/bin/conda env update -p /packages/apps/fsl/6.0.6 -f fsl-6.0.6_linux-64.yml

When running the command without a mamba environment, using the python=3.6.8 from /usr/bin/python, I got a new error: link.

I also tried python=3.11.5 without a mamba env, and it gives the same error as above.

Could you help me take a look at these errors?

Thanks,
Nil

paulmccarthy · June 19, 2024, 8:06am

The latest issue seems to be that your hard drive is out of space - can you clear some space (I’d recommend having at least 15GB free), and try again?

You shouldn’t need to set up a conda/mamba environment in advance - you should just be able to use any python interpreter to run the fslinstaller.py script. FSL will set up its own conda environment(s) during installation.

Nil · June 24, 2024, 7:03pm

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

maryam.riazi · July 25, 2024, 11:19pm

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:

python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
logfile
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

paulmccarthy · July 26, 2024, 8:37am

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

maryam.riazi · July 26, 2024, 3:04pm

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?

paulmccarthy · July 26, 2024, 3:21pm

Hi @maryam.riazi, sorry - I didn’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

maryam.riazi · July 26, 2024, 4:01pm

Thanks @paulmccarthy
I specified another location and it worked!

Rufeyda_Yagci · August 2, 2024, 9:37pm

Hey, hope you are doing well.

My computer be able to install first 2 step ( downloading and installing miniconda) but couldn’t do last step: Installing FSL. It doesn’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

paulmccarthy · August 5, 2024, 9:09am

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 shouldn’t happen in the future.

Rufeyda_Yagci · August 6, 2024, 8:35am

It worked! Thank you so much

seokblim · August 10, 2024, 8:44pm

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 FSL…
Could you please give me your advice to install FSL software?

I attached my log below.
Log Link

paulmccarthy · August 13, 2024, 10:30am

Hi @seokblim, I’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 don’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