Skip to content

Latest commit

 

History

History
60 lines (34 loc) · 2.5 KB

README.md

File metadata and controls

60 lines (34 loc) · 2.5 KB
Raw

Quick Guide for Running GIRFReco Example

You can find code details of the example script here.

System Configuration

Though compatibility with older versions of Julia may exist, our testing environment is Julia with version 1.9.3, and we recommend to use the same or newer version of Julia.

We also recommend to leave at least 30 GB disk space for the example data and all dependent Julia packages.

The reconstructed Cartesian and Spiral images in NIfTI format will be in the folder joss_data_zenodo/results. We recommend to use FSLeyes as the viewer to open them.

Steps of Running the GIRFReco Example

(1) Cloning the package

Download or clone the repo to your local by:

git clone [email protected]:BRAIN-TO/GIRFReco.jl.git

Then enter the example folder:

cd GIRFReco.jl/example

Alternatively, for the one who are using Visual Studio Code, simply open the example sub-folder from the Menu option File -> Open Folder....

(2) Run in Julia REPL

We recommend to use Visual Studio Code with Julia extension (steps of installation can be found here) to avoid possible image displaying issue, especially for those using SSH and X11 forwarding.

The Julia REPL can be launched from the Command Palette (For Windows and Linux: Press Shift + Ctrl + P; For Mac: Press Shift + Command + P) by searching the command Julia: Start REPL.

In the launched REPL, simply execute the following command after launching the REPL to run the whole demonstration script (including the data download):

include("run_example.jl")

If you only want to download the demonstration dataset, run:

include("download_data.jl")

(3) After running your first example ...

"Watch a movie, or be part of one". You are also encouraged to be part of our repo by playing around with the configuration file and see how (and why) the results are changed. For example:

(1) How do the results change when we turn off the B₀ correction (by setting do_correct_with_b0_map as false)?

(2) What will the images look like when we turn off the zeroth and/or the first order GIRF correction (set do_correct_with_girf_k0 and/or do_correct_with_girf_k1 as false)?

(3) Try reconstruction with multiple spiral interleaves by enabling line 97. What changes do you see?

And so many more options to explore...