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 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/
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/
