Pypes includes a CLI to help you with result check-up and analysis.
It is called: nitap.
To check what it is capable of run: nitap -h.
To indicate sets of files in the output folder, it uses hansel.Crumb
notation, see it in the examples below.
Produces a report with plots of the resulting brain images.
You can plot the images in pairs of background and foreground, and it also allows you to choose the number of slices you want.
Example:
nitap plot --bg "/data/hansel/cobre/{sid}/{session}/anat.nii.gz" --fg "/data/hansel/cobre/{sid}/{session}/mni_in_anat_space.nii.gz"
Produces a Excel spreadsheet with the result from RAPIDArt for all pre-processed fMRI subjects.
The value of the crumb arguments in the input path will be also put in the spreadsheet.
Example:
nitap motion -i "/home/alexandre/data/nuk/out/{group}/{sid}/session_0/rest/artifact_stats" -o motion.xls