Lesson 2 - A practical introduction to Gadgetron

Open 2 terminals. Ensure you are in the Lesson_2 directory for each and execute code below:

cd ./learn-gadgetron/learn/tutorial2020/Lesson_2
source ../defineAliases.sh

Note that the defineAliases.sh binds local folders to internal folders in the Singularity container. So /mnt in the container maps to the current directory i.e. ./learn-gadgetron/learn/tutorial2020/Lesson_2 and /media in the container maps to the data folder for the tutorial at ../Gadgetron-2020-summer-school-data

In one terminal start the gadgetron server

source ../defineAliases.sh
startServer

In a second terminal open ismrmrdviewer and hdfview:

source ../defineAliases.sh
viewer /media/Day-1/Lecture-2/simple_gre.h5 &
# after opening hdfview navigate to file and open simple_gre.h5 at location above
hdfview &
# this startst the custom visualization code 
alias gtronvis="gtron visualize" 
gtronvis &

In this terminal we will :

gtronclient -f /media/Day-1/Lecture-2/simple_gre.h5 -C /mnt/config-fixed.xml