MRI phase Processing

Tutorials about processing MRI phase

1: Quantitative Susceptibility Mapping
2: SWI
3: Unwrapping

1 - Quantitative Susceptibility Mapping

Example workflow for Quantitative Susceptibility Mapping

This tutorial was created by Steffen Bollmann and Ashley Stewart.
Github: @stebo85; @astewartau Web: mri.sbollmann.net Twitter: @sbollmann_MRI

Getting Setup with Neurodesk

For more information on getting set up with a Neurodesk environment, see here

An example notebook can be found here: https://www.neurodesk.org/example-notebooks/structural_imaging/qsmxt_example.html

Please see the above example notebook which provides a detailed QSM tutorial using QSMxT.

2 - 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)

3 - Unwrapping

MRI Phase Unwrapping

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/


mkdir /neurodesktop-storage/romeo-demo/

cp /neurodesktop-storage/swi-demo/01_bids/sub-170705134431std1312211075243167001/ses-1/anat/sub-170705134431std1312211075243167001_ses-1_acq-qsmPH00_run-1_phase.nii.gz /neurodesktop-storage/romeo-demo/phase.nii.gz

cp /neurodesktop-storage/swi-demo/01_bids/sub-170705134431std1312211075243167001/ses-1/anat/sub-170705134431std1312211075243167001_ses-1_acq-qsm_run-1_magnitude.nii.gz /neurodesktop-storage/romeo-demo/mag.nii.gz

gunzip /neurodesktop-storage/romeo-demo/mag.nii.gz
gunzip /neurodesktop-storage/romeo-demo/phase.nii.gz

Using ROMEO for phase unwrapping

Open the ROMEO tool from the application menu and run:

romeo -p /neurodesktop-storage/romeo-demo/phase.nii -m /neurodesktop-storage/romeo-demo/mag.nii -k nomask -o /neurodesktop-storage/romeo-demo/

Romeo