1.0 Create pseudo CT images

1. Download the NIFTI images for your T1 sequence
   • Go to Project > Actions > Download images
   • Select sessions, scan data type (NIFTI), scan type (Fig.1)

   Fig.1 Download NIFTI images.

   • Unzip the archive. To extract the compressed NIFTI files from the directory structure, run command from the data folder: cp ./*/*/NIFTI/*.gz ./

1. Upload the NIFTI files to CT synthesis tool (Fig.2)
   • Go to http://niftyweb.cs.ucl.ac.uk/program.php?p=PCT
   • Enter email, select Input Image Modality T1-weighted MRI, Parameters Optimise for accuracy
   • Select 5 files at a time
   • It takes about an hour for one file to process

   Fig.2 Online CT synthesis tool.

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