Code: Click here to request.
Zöllei, L, Iglesias, J.E., Ou, Y. Grant, P.E., Fischl, B.: Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years; arXiv:2001.03091 https://arxiv.org/abs/2001.03091
Zöllei et al. FreeSurfer image processing pipeline for infant clinical MRI images. Human Brain Mapping, Vancouver, Canada, 2017.
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!