Closed CogBrainHealthLab closed 4 months ago
If you install a conda environment with conda env create -f env.yml
, then a compatible version of FSL will get installed there. You can set the $FSLDIR
environment variable to look there for its FSL tools.
$ conda env config vars set -n fmriprep FSLDIR=$(conda activate fmriprep && echo $CONDA_PREFIX)
Actually, MSM isn't distributed with FSL, so this is a different problem. You need to get MSM from https://github.com/ecr05/MSM_HOCR/releases/.
Here's what we do in Docker:
You could drop that into your fmriprep environment:
$ MSM=$(conda activate fmriprep && echo $CONDA_PREFIX)/bin
$ curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/ecr05/MSM_HOCR/releases/assets/16253707 -o $MSM
$ chmod +x $MSM
What happened?
the fmriprep run on a single subject completed with an error specific to the FSL msm command. I realized that the configuration parameters used in site-packages/smriprep/data/msm/MSMSulcStrainFinalconf no longer work when FSL 6.0.7.11 is installed. More specifically, the following msm configuration options no longer exist
--regoption=3 --dopt=HOCR --triclique --k_exponent=2 --bulkmod=1.6 --shearmod=0.4
I understand that i am supposed to use FSL 6.0.6.2 instead of FSL 6.0.7.11, but the latest version was installed in my HPC cluster, so i have to make do with it.
so would you suggest i comment out these options, or simply run fmriprep with --no-msm?
What command did you use?
What version of fMRIPrep are you running?
23.2.3
How are you running fMRIPrep?
Local installation ("bare-metal")
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
FreeSurfer
Please copy and paste any relevant log output.
Additional information / screenshots
No response