valosekj

Simple workflow of collaboration in small team using git and GitHub

This gist describes example of simple workflow on repository whose changes are tracked by git and GitHub

1) Clone (download repository from GitHub to your computer)

# Go to directory where repository will be cloned (downloaded)
cd ~/Documents
# Clone repository from GitHub

valosekj

Configuration of ssh connection

Unix and MacOS

Let's say we want to configure an ssh connection between machine alpha and beta.

1. Go to your home folder at machine alpha:

$ cd ~

valosekj

# Set ITK direction from image1 to image2
#
# Usage:
#	python change_itk_orientation.py <image1> <image2>
# Example:
#	python change_itk_orientation.py sub-001_T1w.nii.gz sub-001_T1w_seg.nii.gz
#
# Jan Valosek
#

valosekj

import os
import glob
import hashlib
import argparse


def compute_checksum(file_path):
    with open(file_path, 'rb') as f:
        file_bytes = f.read()
    return hashlib.md5(file_bytes).hexdigest()

valosekj

Template script for sct_run_batch

This gist contains a template script that can be run across multiple subjects using the sct_run_batch wrapper script.

The template bash script below can be run from you command line using the following command:

sct_run_batch -script example_script.sh -path-data <DATA> -path-output <DATA>_202X-XX-XX -jobs 16

valosekj

valosekj

Load a Python colormap to FSLeyes

Get RGB colors, one per line, for a given Python colormap. In the script below, we get RGB colors for the jet matplotlib colormap.

import matplotlib.pyplot as plt
import numpy as np

# Generate the jet colormap
cmap = plt.cm.get_cmap('jet')