| # A little helper to show /om usage information for user + group, | |
| # as well as some SLURM usage | |
| # For easiest use - add function to .bashrc that sources this with a simple input | |
| import subprocess | |
| from getpass import getuser | |
| from collections import Counter | |
| import re |
| submit_mindboggle.sh | |
| ------------------------------------------------------------------- | |
| #!/bin/bash | |
| base={{FULL PATH TO DATA}} | |
| # first go to data directory, grab all subjects, | |
| # and assign to an array | |
| pushd $base | |
| subjs=($(ls sub-* -d -1)) # this is set up for BIDS, but you can alter the search pattern |
| import os | |
| def create_key(template, outtype=('nii.gz'), annotation_classes=None): | |
| if template is None or not template: | |
| raise ValueError('Template must be a valid format string') | |
| return (template, outtype, annotation_classes) | |
| def infotodict(seqinfo): | |
| """Heuristic evaluator for determining which runs belong where |
| #!/usr/bin/env python | |
| import pandas as pd | |
| import numpy as np | |
| from argparse import ArgumentParser | |
| import sys | |
| import os | |
| def parse_outliers(outliers, volumes): | |
| if not outliers: |
| import asyncio | |
| import concurrent.futures as cf | |
| # from multiprocessing.context import ForkServerContext | |
| import time | |
| import functools | |
| # used to bypass Event Loop error in Jupyter Notebooks | |
| import nest_asyncio | |
| nest_asyncio.apply() |
| from pydra import mark, Workflow | |
| @mark.task | |
| def add1(x): | |
| return x + 1 | |
| # start workflow | |
| wf = Workflow(name='wf', input_spec=['x']) | |
| wf.inputs.x = 2 |
===================================
fMRIPrep has adopted cal-sem versioning. This can be broken down by the following example, X.Y.Z.e, where:
X = major version, signals year of the release. A release from 2020 will start with a 20. major version. Y = minor version, signals API breaking and/or output altering changes. Upgrading minor version will not be backwards compatible. Z = patch version, AKA bug fix releases. Patch versions will be backwards compatible with all minor version releases.
| import os | |
| import nibabel as nb | |
| import numpy as np | |
| from nipype.interfaces.base import isdefined | |
| from nipype.interfaces import fsl, ants, afni | |
| import nipype.pipeline.engine as pe | |
| from niworkflows.interfaces.registration import ( | |
| EstimateReferenceImage, |
