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Code: Click here to request.
Cite:
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).
Current skullstripping code: PICASSO -- need to get it independently, from NITRC. With questions related to this tool, contact Dr Ou ( yangming.ou@childrens.harvard.edu ).
EXECUTION
setenv MATLAB_ROOT PATH_MATLAB_8.0_INSTALLATION
source set_babydev_packages.csh
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 MATLAB (recommended version is 8.0), 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