Regarding attenuation correction, you should provide an attenuation image (interfile format) of the jaszczak phantom in cm-1 unit to the castor-recon executable (assuming your GATE data has been converted to list-mode, which is selected by default for data converted from GATE). Note that the conversion utility (castor-GATERootToCastor) also contains an -atn option, which is only to use if you want an histogram dataset.
There is currently no tools to automatically compute normalization correction factors. You could generate a normalization datafile (see the documentation, section 6.1.2) for your GATE data using this kind of method: https://ieeexplore.ieee.org/document/6153804. Alternatively, you could directly generate a sensitivity image containing normalization corrections using a GATE simulation of an uniform object spanning the whole field of view of your system. Then, you provide this image to castor-recon using -senspath/to/your_sensitivity_image.hdr to bypass the sensitivity image generation step and use your image instead). However, this approach should be less accurate.
Finally the error you get means the code can’t find the scanner repository, which is apparently located at */GATE/castor_v.2.0.2/*castor_v2.0.2/config/scanner in your system. You should check if the path is correct (no typo?).
