Information

Bundle of bash, python and matlab scripts and functions used in routine work.

General functions:

Used within another scripts for checking input, running commands, logging etc.

check_input - script for checking existency of directories or files

exe - script for execution certain command and prints its output to log

show - script for printing messeage or command's output in various ways (e.g. like ERROR in red color)

Functions for monitoring of running processes:

Used for monitoring of running processes.

get_elapsed_time - get elapsed time based on processID (pid)

exe_kill - execute certain command, monitor it and kill if it runs over time limit

wait_then_kill - monitor process based on its pid and kill it if the process run longer than set time limit (can be called from exe_kill)

kill_process - kill process based on processID (pid)

get_pid_and_name - get pid and full process name based on process name

get_pid - get pid based on process name

Functions for working with DWI data:

Used for manipulation with diffusion-weighted MRI data (dMRI/DWI)

prepare_topup_file - create a text file for FSL's topup function

prepare_eddy_file - create a text file for FSL's eddy function

get_unique_bvals - get unique b-values from input bval file

count_bvals.py - python script for counting number of DWI volumes acquired with given b-value

separate_b0_and_dwi - separate b0 and DWI volumes from 4D diffusion image

create_dummy_b0_bval_and_bvec - create dummy bval and bvec files with zeros

merge_bval_bvec_files - merge bval/bvec files into one

parse_SliceTiming_from_json.m - matlab function for fetching of SliceTiming parameter from .json (used for --slspec flag of FSL's eddy)

display_bvecs.m - matlab function for simple 3D visualisation of gradient vectors based on bvec file

Functions for working with MRI data headers:

parse_dicom_header.sh - parse dicom header and fetch specific tags (this script requires AFNI dicom_hdr function)

compare_nifti_headers.sh - compare headers of two input nifti files

Some other functions/scripts:

get_ip_adress - print hostname and IP adress to CLI

run_matlab - script for running matlab from command line without opening MATLAB desktop

send_email_when_finish - send email when process finish

and some others, see other_tools folder

Usage:

Clone (download) repo:

cd ${HOME}/code
git clone https://github.com/valosekj/bash_basics.git

Note: I recommend to clone the repo into ${HOME}/code directory

Usage inside scripts

Include following lines into your script:

source ${HOME}/code/bash_basics/config_bash.sh

export LOGPATH=./log.txt
exec > >(tee -a $LOGPATH) 2>&1

Usage in terminal/CLI

You can source this repo within your bashrc/zshrc file to be able to use functions in CLI:

# Add following lines to your ${HOME}/.bashrc or ${HOME}/.zshrc file
source ${HOME}/code/bash_basics/config_bash.sh

Contact:

Jan Valosek