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** Updates 02/10/2020:

a new version of the infant pipeline has been created for your use. See below for details about the new features.

EXECUTION

The most basic command line that you can run in order to execute the pipeline is the following.

setenv SUBJECTS_DIR your_data_path      ** OR **    export SUBJECTS_DIR=your_data_path

infant_recon_all --s SUBJ --age age_in_months

You can run this release from both tcsh or bash.

Just like before, 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. One example would be using

mri_nu_correct.mni --i $infile --o $nufile --n 2


** Below are Notes from the original release **

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

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

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!

infantFS (last edited 2020-08-14 04:47:43 by LillaZollei)