I am just asking for some tips to make the brain more beautiful that the raw results from SPM, Freesurfer, FSL or other neuroimaging softwares. I have tried BrainNet Viewer (toolbox implemented in Matlab) or Caret and I would like to know if you usually use other tools. For example, I try desperately to make a small sphere above one specific voxel and it is such a pain.
Python tools, Matlab tools, Fortran tools whatever, everybody is welcome
I think you should give a try to ANTsR, the R-package where you can show that small sphere on a 3d glass brain.
For surface rendering I would suggest Surf Ice, which can display many formats including those used by SPM, FreeSirface, FSL, MRTrix and BrainNet Viewer. For volume rendering I would suggest MRIcroGL which can view voxel data generated by FSL, SPM and other tools. Both programs run natively on Windows, MacOS and Linux and include a scripting language so you can control them either using the GUI or automate them in your pipeline.
I would suggest “Pysurfer” too !
It is a Python library for visualizing cortical surface representations
PySurfer extends Mayavi’s powerful rendering engine with a high-level interface for working with MRI and MEG data.