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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]. Before execution, you will need install `FSL` [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation] and `dramms` [www.nitrc.org].


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).

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 ).


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 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

infantFS (last edited 2022-04-18 13:50:58 by PaulWighton)