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 here

Download 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)