PET to MR registration via CT

Preprocessing and extraction of data from regions in a PET image, using FSL. Regions are derived from a MultiAtlas segmentation (https://github.com/VUIIS/Multi-Atlas-v3.0.0, https://github.com/MASILab/SLANTbrainSeg).

1. Motion correction applied to PET time series (mcflirt, 6 dof)
2. CT registered to mean PET (flirt, 6 dof)
3. Mean PET registered to MR (flirt, default 6 dof)
4. SUVR calculated from summed PET image, referenced to cerebellum
5. PET regional values extracted with nilearn

Inputs

The command line is

petreg.sh <arguments>

And <arguments> are below. The first four are required:

--pet_niigz       PET time series
--ct_niigz        CT
--mr_niigz        MR (typically T1W)
--seg_niigz       Segmentation of MR from multi-atlas / slant

--petmr_dof       DOF for PET/MR registration (default 6)

--project         Information from XNAT, if used (optional). These
--subject           are only used to annotate the PDF QA report.
--session
--scan

--out_dir         Where outputs will be stored (default /OUTPUTS)

--labels_csv      Labels corresponding to seg_niigz. Optional argument
                    only needed in special circumstances.

Outputs

All output images have been resampled to the field of view, voxel size, and geometry of the MR.

CT_REG                   CT registered to MR
CT_REG_MAT               Transform from CT to MR (FSL format)
MEANPET_REG              Mean PET registered to MR
MOT_PARAMS               PET time series motion parameters (FSL format)
PDF                      QA report
PET_REG                  PET time series registered to MR
PET_REG_MAT              Transform from PET to MR (FSL format)
PET_ROI_MEANS            ROI means of PET time series
PET_ROI_SDEVS            ROI std devs of PET time series
ROIS                     ROI image
ROI_LABELS               ROI label names
SUM_REG                  Sum of PET images over time
SUM_ROI_MEANS            ROI means of summed image
SUM_ROI_SDEVS            ROI std devs of summed image
SUVR_REG                 SUVR image calculated from summed image
SUVR_ROI_MEANS           ROI means of SUVR image
SUVR_ROI_SDEVS           ROI std devs of SUVR image

References

• FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
• MCFLIRT: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT
• FLIRT: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT#References
• nilearn: https://nilearn.github.io/authors.html#citing
• MultiAtlas: https://pubmed.ncbi.nlm.nih.gov/23265798/
• SLANT: https://pubmed.ncbi.nlm.nih.gov/30910724/