Problems installing FSL

yuhan_chen · January 22, 2024, 3:21pm

Hi @paulmccarthy , I am currently attempting to install FSL on Ubuntu 22, and I have encountered an issue where the installation process has been stuck at 12% for over two hours, as indicated below. I was wondering if you might have any suggestions or advice for this situation, or should I continue waiting patiently without taking any further action?

paulmccarthy · January 23, 2024, 9:04am

How fast is your internet connection? The installation involves downloading around 4GB of data, so if you are using a slow connection it is going to take a long time.

yuhan_chen · January 23, 2024, 1:50pm

Thanks for the info. I’m not entirely certain about the stability of my network connection. I have to use a proxy due to server firewalls, which gives me an average download speed of about 1MB/s when downloading Miniconda. As for FSL, I haven’t been able to gauge the speed since it lacks a progress bar.

Is there an alternative to the standard installation scripts? Like pre-downloading the source code for local compilation. Also, I’m exploring other options, like the impressive fslpy project, though I’m still learning about its capabilities and usage. I’m relatively new to this field and my main goal is to preprocess fMRI data (like motion and slice-timing correction) for analysis. Any guidance or suggestions would be greatly appreciated!

Steven · January 23, 2024, 1:58pm

Hi @yuhan_chen,

You can try using one of the Docker containers. E.g.,: Docker

You can try fmriprep for that fMRIPrep: A Robust Preprocessing Pipeline for fMRI Data — fmriprep version documentation (also works off of Docker/Singularity containers). The developers often provide help for that on this website.

Best,
Steven

yuhan_chen · January 23, 2024, 2:10pm

Hi @Steven,

Thank you very much for your helpful suggestions! I’ll try using the Docker containers and fMRIPrep right away.

Best regards,
Yuhan

juan · January 26, 2024, 6:34pm

Hello,
Apple Silicon m3 with MacOS Sonoma 14.3. (Should work with all M1, M2 and M3). Following these steps I could install FSL correctly. All thanks to @aymen_meddeb’s hint. Hopefully this post can be helpful for others. The problem seems to be due to some incompatibility between Anaconda’s mamba package installed by default in base environment and the mamba package specified by FSL’s installation. So a regular python installation, rather than Anaconda, should also probably work. But, in case you just want it to work and you are an Anaconda user…

Create an empty python environment (you can specify your own python version or none at all). This is only needed for the installation process. Once FSL is correctly installed you can go back to your regular python envs.

conda create --name fsl_install_env python=3.11

Activate it.

conda activate fsl_install_env

run the installation script. No need to specify flags like --conda etc… Your actual command might be different, but should be similar to.

python fslinstaller.py

When FSL is correctly installed, you can activate your previously active env and delete this one. To properly configure FSL you can open a new terminal and call FSL, as specified in FSL’s installation instructions.

fsl &

or

fsleyes &

should work.

Hope this helps.

Kvandeloo · February 1, 2024, 9:07pm

Hi Juan,

I get this error as well, even after trying your fix. I have an Intel based Mac, and am currently using miniconda3. Do you have any insight?

Thank you!

Tru_Gamble · February 4, 2024, 4:44pm

@paulmccarthy

I am having a similar issues as the others when trying to download FSL.

Ive tried both mamba and conda, but I get an error message after only a minutes. It also never goes above 0% downloaded.

I’ll included the error message I keep getting.

paulmccarthy · February 5, 2024, 9:48am

Hi @Kvandeloo and @Tru_Gamble, can you both please share the installer log file?

Tru_Gamble · February 5, 2024, 6:52pm

Here it is.

paulmccarthy · February 6, 2024, 9:51am

It looks like you’ve attached the installer script itself, not the log file that is mentioned in the output you pasted earlier.

Kvandeloo · February 8, 2024, 4:31pm

@paulmccarthy

FYI I’m using a 10-core i9 iMac w/ 128GB RAM, with miniconda3

Command:

Log:

paulmccarthy · February 8, 2024, 4:47pm

Hi @Kvandeloo, could you please:

Re-download the fslinstaller.py script from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
Re-run this new version without the --conda option
and, if it doesn’t work, report back what happens (including the log file)?

Tru_Gamble · February 9, 2024, 12:08am

Ah yeah oops. I am having a different issue now though. It starts installing but is getting stuck at 92%.

Tru_Gamble · February 9, 2024, 12:24am

Ok I tried to re-install it, but it said the package was already on my device…
I think this was the log file you were referring to though.

Kvandeloo · February 9, 2024, 1:48am

Hi @paulmccarthy ,

Here is the prompt:

And the log:

paulmccarthy · February 9, 2024, 12:15pm

Hi @Kvandeloo, could you try running the installer (the new version that you downloaded) with this command:

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

paulmccarthy · February 9, 2024, 12:17pm

Hi @Tru_Gamble, could you re-download the fslinstaller.py script from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py, and re-run it with this command (it should report itself as being version 3.8.2):

python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh

Aflah_Jamal · February 10, 2024, 10:01am

Hey @paulmccarthy, thanks a lot.
This works.

My macbook air OS14-Sonoma was having same problem like @Tru_Gamble had which fsl installation stopping at 92%. I have tried all other above solutions like
1)creating new env(stopped at 92%)
2) --conda(stops before starting fsl installation)
nothing works.

Finally this works.

Kvandeloo · February 19, 2024, 2:33am

Thanks so much - this worked!