Hello,
I have troubles installing FSL on my MacBook Air M2, OS Sequoia 15.2
I downloaded the flinstaller.py that i compiled in my terminal using python/python3, either in my downloads file or a Users/myname/softwares/ repository i created
I keep getting stuck at the 3rd step of installation : Installing FSL into /Users/asavalle/softwares/fsl/v…
3 / 3 [ ] 0 / 100 % |
i get a similar error message each time, no matter the conda environment with good version of python, or the repository, or using --conda or not. Is there anything i could do ?
as i cannot add any attachment file bc i am a new user, here are 2 screenshots of the last lines of the log file :
Hey @paulmccarthy sorry for this late answer. Thank you for your answer.
I tried installing fsl with the command you gave me, and then with miniconda installed directly on my computer, also tried using conda, and using advices given in : Problems installing FSL - #30 by Tru_Gamble such as doing the installation in a created conda environment.
I always end up with the same problem : the 3rd step of installation stuck at 0% and an error message with the log file mentioning "/Users/asavalle/Dev/fsl/bin/conda env update -p /Users/asavalle/Dev/fsl -f fsl-6.0.7.16_macos-M1.yml . ". I have no trace of this yml file, maybe there is something i could do there ? Thank you in advance for your help
Hi @adele, I’ve fixed a bug in the script - can you re-download it again, and try running the command from my previous message? The flag is --miniconda, not --micromamba.
For posterity, we will be soon be switching to micromamba by default, at which point it will not be necessary to pass the URL to a specific micromamba installer.
Hi.
I finally managed to install fsl 6.0.7.16 on a Rocky linux cluster using this method. I used FSL installer version: 3.16.3. However, it did not work when I tried installing it with -e truenet, just worked without it.
I am also unable to add truenet with update_fsl_release --extra truenet (adding --cuda 12.1 or not adding it did not change the outcome). it complained about not finding conda or mamba executables in $FSLDIR/bin. I symlinked micromamba which was there as mamba but then it just fails
without complaining about conda/mamba.
File “/work//fsl/lib/python3.12/site-packages/fsl/installer/fslinstaller.py”, line 1343, in monitor_progress
raise RuntimeError('This command returned ’
RuntimeError: This command returned an error: /work/zhang_lab/Shayan/fsl/bin/mamba env create -p /work//fsl/envs/truenet -f fsl-6.0.7.16_truenet_linux-64.yml
adding --miniconda as suggested above to fsl_update_release or fslinstaller.py was not was not helpful either for truenet.
Hi @shneuro, your timing is slightly unfortunate - I have added preliminary support for micromamba to the fslinstaller.py script, but the update_fsl_release command does not yet support micromamba. Can I ask what issues you were encountering when running the fslinstaller.py command normally (i.e. without --miniconda <url>)?
Hey @paulmccarthy – I’m having a similar problem and I’ve tried the fixes in this thread. Any suggestions? I’m on Mac OS 15.2. I cannot upload the log but got an error at Stage 4 (pasted below). Thanks!
ERROR occurred during installation!
This command returned an error: /Users/CHOIKX9/fsl/bin/conda env update
@shneuro@ypathak I really need to be able to see your log file to help. If you can’t upload it here, you can use any file sharing service of your choice (dropbox, google drive, onedrive, etc).
