SWI
Example workflow for SWI processing
This tutorial was created by Steffen Bollmann.
Github: @stebo85 Web: mri.sbollmann.net Twitter: @sbollmann_MRI
Getting Setup with Neurodesk
For more information on getting set up with a Neurodesk environment, see hereDownload demo data
Open a terminal and run:
pip install osfclient
cd /neurodesktop-storage/
osf -p ru43c fetch 01_bids.zip /neurodesktop-storage/swi-demo/01_bids.zip
unzip /neurodesktop-storage/swi-demo/01_bids.zip -d /neurodesktop-storage/swi-demo/
Open the CLEARSWI tool from the application menu:
paste this julia script in a julia file and execute:
cd /neurodesktop-storage/
vi clearswi.jl
hit a or i and then paste this:
using CLEARSWI
TEs = [20]
nifti_folder = "/neurodesktop-storage/swi-demo/01_bids/sub-170705134431std1312211075243167001/ses-1/anat"
magfile = joinpath(nifti_folder, "sub-170705134431std1312211075243167001_ses-1_acq-qsm_run-1_magnitude.nii.gz")
phasefile = joinpath(nifti_folder, "sub-170705134431std1312211075243167001_ses-1_acq-qsmPH00_run-1_phase.nii.gz")
mag = readmag(magfile);
phase = readphase(phasefile);
data = Data(mag, phase, mag.header, TEs);
swi = calculateSWI(data);
# mip = createIntensityProjection(swi, minimum); # minimum intensity projection, other Julia functions can be used instead of minimum
mip = createMIP(swi); # shorthand for createIntensityProjection(swi, minimum)
savenii(swi, "/neurodesktop-storage/swi-demo/swi.nii"; header=mag.header)
savenii(mip, "/neurodesktop-storage/swi-demo/mip.nii"; header=mag.header)
hit SHIFT-Z-Z and run:
julia clearswi.jl
Open ITK snap from the Visualization Application’s menu and inspect the results (the outputs are in swi-demo/swi.nii and mip.nii)
