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