Jan Valosek 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

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

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

$ cd ~

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

Note

You can directly pass the name of an matplotlib colormap to FSLeyes on the command line, for example:

fsleyes sub-001_T2w_rootlets.nii.gz -cm Jet

Download Xcode from the App Store
Opan a new Terminal tab and run sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer
Accept the Xcode licence by running: sudo xcodebuild -license
Try running /usr/bin/xcodebuild -version to ensure Xcode is correctly installed and configured
Create a new conda env and install pytorch-nightly:

conda create -n nanogpt python=3.10

Install the Continue plugin:

PyCharm --> Settings --> Plugins --> search for "Continue" --> Install
Download and install Ollama
Download some LLM model, which can be run locally. For example, the open-source Granite model from IBM:

	# 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
	#

	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()