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Convert photos from HEIF to JPEG

I use on my iPhone HEIF (High Efficiency Image File Format) format for storing my photos.

This format is widely supported throughout Apple ecosystem but sometimes I need to quickly convert photos from HEIF to JPG to be able to use these photos also elsewhere (Windows, some websites, etc.)

I use for this purpose convert command line tool from ImageMagick

Usage:

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Useful shell commands

This gist contains several useful shell commands which I use frequently during my work.

$0 - Get current shell

$ echo $0
zsh

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Run matlab function from python script

I needed to run matlab script from python script. I wanted to pass several input arguments from pandas DataFrame, perform calculation in matlab and return multiple output arguments back to python.

Steps (MacOS):

1. Install matlab engine API for python:

In your terminal, go to directory where matlab is install and run installation python script, e.g.:

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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 ~

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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

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# 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
#

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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()

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Run arbitrary application from terminal on MacOS

Sometimes, it is convenient to have possibility to start/run any application (like your internet browser or text editor) directly from your terminal. Most of these applications however do not create shortcut for easy run from terminal during their installation. Below is short manual how to create this shortcut manually.

Steps

1. Open terminal (cmd + space --> type terminal)

2. Navigate to a directory where you have your code/scripts. For example ~/code or /usr/local/bin:

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Run python script from shell (bash, zsh)

Sometimes, I need to call/run python script with arguments from shell. I use bash or zsh as my shell and following workaround works great for me.

Using shell wrapper

1. Some example python script which I need to run from bash:

my_python_script.py:

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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