Code: Click here to request.
Zöllei et al. FreeSurfer image processing pipeline for infant clinical MRI images. Human Brain Mapping, Vancouver, Canada, 2017. (until journal submission is still under review)
de Macedo Rodrigues, K., et al., A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range. Front. Hum. Neurosci., 2015. 9(21).
setenv SUBJECTS_DIR your_data_path
infant_recon_all --s SUBJ --age age_in_months
Note, run everything from tcsh. Bash scripts are not yet ready for this distribution.
Before execution, you will need install FSL [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation] and dramms [www.nitrc.org].
The script will expect the input file to be located at $SUBJECTS_DIR/$subj/mprage.nii.gz or $SUBJECTS_DIR/$subj/mprage.mgz by default. If the --masked flag is used, we recommend also running intensity normalization using
mri_nu_correct.mni --i $infile --o $nufile --n 2
Other useful flags:
--masked (using a skullstripped input)
--outdir (redirecting output)
--kneigh (number of training examples to use)
See infant_recon_all --help for more information
NOTES Currently, aparc is provided for sake of completeness, but has not been fully validated. It is a projected version of the adult atlas, so it does not originate from the infant training data set!