Import fmriprep output¶
Recently, many people have start to use fmriprep as a complete preprocessing workflow of anatomical and functional data. Pycortex has a convenience function to import the output of this workflow.
This example is based on the fmriprep 1.0.15 output of openfmri ds000164 that can be found on openneuro.org: https://openneuro.org/datasets/ds000164/versions/00001
NB: cortex.fmriprep is a work-in-progress and cannot currently handle multiple datasets when the subject IDs are the same (see https://github.com/gallantlab/pycortex/issues/304).
import cortex from cortex import fmriprep from os import path as op # Location of the downloaded openfmri dataset source_directory = '/derivatives/ds000164' # fmriprep subject name (without "sub-") subject_id = '001' # import subject into pycortex database fmriprep.import_subj(subject_id, source_directory) # We can use visualize the imported subject's T1-weighted image anat_nifti = 'fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz' t1_image_path = op.join(source_directory, anat_nifti) # Now we can make a volume using the built-in identity transform t1w_volume = cortex.Volume(t1_image_path, subject_id, 'identity') # And show the result. ds = cortex.Dataset(t1w=t1w_volume) cortex.webgl.show(ds)
Total running time of the script: ( 0 minutes 0.000 seconds)