Centralized, simple, searchable recipes (code snippets) for neuroimaging data

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• Using 3dcalc to create a binary mask from a parcellation scheme

  This recipe uses 3dcalc in AFNI to output a binarized 3D image file (nifti) of a region-of-interest in a parcellation scheme that is indexed … Read More

• BIDS Validation Recipe

  Validating BIDS formatted Datasets using bids-validator Command Line Tool This recipe uses the bids-validator v1.5.7 command line tool to … Read More

• Convert DICOM files to NIFTI files

  This recipe provides code for converting DICOM (.dcm) files to NIFTI (.nii) files dcm2niix This recipe converts dicom to nifti files using … Read More

• Mask lower triangle of a Representational Dissimilarity Matrix (RDM)

  This recipe takes a Representational Dissimilarity Matrix (RDM) as a square numpy array, masks the diagonal and lower triangle, and outputs … Read More

• PyDeface Recipe

  Defacing Multiple Brain Imaging Modalities using PyDeface For this recipe, we are using pydeface-2.0.0. Ingredients: A python environment … Read More

• Using 3dAFNItoNIFTI to convert AFNI files to NIFTI files

  This recipe converts BRIK/HEAD (AFNI) files to NIFTI (.nii) files using 3dAFNItoNIFTI. … Read More

• Automatically Generated Recipe

  Explain briefly what the recipe does. Explain briefly how the recipe works. Provide a citation and link to documentation of any third party … Read More