FMRIprep

module load singularity-fmriprep

fmriprep is installed as a singularity container. By default it will always run the current latest version. If you need a version that is not currently installed on triton, please open an issue at https://version.aalto.fi/gitlab/AaltoScienceIT/triton/issues

To run fmriprep for one subject, without free-surfer reconall, using ica-aroma

singularity_wrapper exec fmriprep <path-to-bids> <your-scratch-folder> participant --participant-label 01 --use-aroma --fs-no-reconall --fs-license-file /scratch/shareddata/set1/freesurfer/license.txt

POST-processing

Fmriprep does the minimal preprocessing. There is no smoothing, no temporal filtering and in general you need to regress out the estimated confounds. The most simple way is:

module load fsl
fsl_regfilt -i $inputniifile -d "$file_with_bold_confounds.tsv" -o $outputniifile -f 1,2,3,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31
There are also tools for post-processing such as:

These are not installed on the singularity image, hence you need to experiment with these on your own.