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Dear Experts,
I am working with FreeSurfer infant_recon_all and I need to correct the pial surface for most of the analyzed subjects. I would like to implement this correction by fixing the intensity normalization using control points, as well as for the adult subjects with tkmedit, but I can not understand if it is then possible to re-run the infant_recon_all pipeline (or how) after the cp definition, since it seems to me that it does not exist the possibility to add -autorecon2-cp and -autorecon3 flags to infant_recon_all, like with the pipeline for adults.
So, I am asking if you have some suggestion to do that. I have already tried to normalize the intensity with flag --intnormFSL, specific for infant_recon_all. The result is better but not the best. Is there any other possibility? For example: - to launch mri_nu_correct.mni --i $infile --o $nufile Then, should I add the --masked flag at the infant_recon_all command by passing $nufile as input? Which is the difference between this one and the --intnormFSL option?
- Is there something similar to the adult -autorecon2-cp also for infants?
- Do you think that the application of AntsN4BiasFieldCorrectionFs is a good idea? And what about the possibility of applying newborn FLAIR sequence to the Bias Field corrected images?
- Could it be better to create my own atlas and to use that to obtain a better segmentation?
Thank you very much for any kind suggestion. Best Regards,
Laura Mazzocchi
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