SPM_datasets/spm_facerep_fmriprep: fmriprep output of the BIDS dataset "face repetition" from SPM

fmriprep output of the BIDS dataset "face repetition" from SPM

Remi Gau bb669a44bf [DATALAD] Recorded changes		2 years ago
.datalad	c40399a4b3 [DATALAD] Remove container fmriprep	2 years ago
derivatives	8e1ec58dad [DATALAD] auto-saved changes	2 years ago
raw @ b2a93028a9	e9deadd851 [DATALAD] Recorded changes	2 years ago
.gitattributes	db75cb154d [DATALAD] new dataset	2 years ago
.gitmodules	e9deadd851 [DATALAD] Recorded changes	2 years ago
README.md	bb669a44bf [DATALAD] Recorded changes	2 years ago

Folder structure

fMRIprep

Install datalad & others in a virtual environment

virtualenv -p python3.8 env
source env/bin/activate
pip install datalad datalad-neuroimaging datalad-container

Get fmriprep (make sure singualrity is installed)

datalad containers-add fmriprep --url docker://nipreps/fmriprep:20.2.0

Run fmriprep

input_dir=`pwd`/raw
output_dir=`pwd`/fmriprep
participant_label=01
freesurfer_licence=~/Dropbox/Softwares/Freesurfer/License/license_1.txt

datalad containers-run -m "fmriprep 01" \
	--container-name fmriprep \
	--input ${input_dir} \
	--output ${output_dir} \
    fmriprep $input_dir ${output_dir} participant \
	--participant-label ${participant_label} \
	-w /tmp --fs-license-file ${freesurfer_licence} \
    --output-spaces T1w:res-native MNI152NLin2009cAsym:res-native

README.md

Folder structure

fMRIprep