Hi Syed
> 1. Downloaded the Marsbar toolbox (0.45). It also has .mat files of defined ROIs in MNI space.
> However, I can only view those ROIs on a template available on SPM, but can't find
> anything where I can apply those ROIs on my own, spatially normalized FDG PET.
If you want to extract the mean intensity from your normalised FDG images, using the marsbar regions, you can do this all in the gui:
Click 'Basic models' on the SPM GUI
For 'Directory' specify output directory
For 'Scans' select your spatially normalised FDG images
From the top menu, choose SPM->Stats->Model estimation
On the Model estimation item, click 'select spm.mat, and the click 'dependency' at the bottom.
Click OK to choose the SPM.mat from the design
Click green arrow. Wait a short while.
This all runs a one sample t test in SPM.
In marsbar gui
'Data' - Extract ROI data (default)
Choose the marsbar regions you want
then select the spm.mat file in the directory from SPM above
'Results' - Estimate results
'Data' -Export Data choose 'summary time course(s) (the starred default)
choose export option
This will produce values for the mean image intensity in your N regions and X images
You can also do various statistical analyses on the ROI values within marsbar, though in that case you would have to choose an appropriate model when you set up SPM in the first place (rather than a one sample t test)
There is a good manual for marsbar on https://marsbar-toolbox.github.io/index.html
> I also built ROIs with coordinates, spheres and had no trouble viewing them on the template
> available on SPM, but couldn't find a way to apply them on my own, spatially normalized FDG PET.
You can use the marsbar ROI definition -> Import ROI to take nifti images and create .mat files, which you can then use in marsbar as above.
Best wishes
Michael
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