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Jason Bowerman authored
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Dependencies

The dependencies for this project can be obtained using the pom file provided. You may also need

  • niftijio.jar
  • niftijlib.jar
  • dcm4che-core-5.23.2.jar

These can be found online but could not be obtained from maven.

Settings File

You will need a settings file in the location of you will run the program from. The following is what the settings file should look like.

    {"projects": {
        "atlas_viewer": {
            "browser_entry": "/path/to/subjects",
            "atlas_base": "/path/to/atlas/dir",
            "quarter_band_count": 4,
            "overlay": {
                "dipole_h": "900",
                "overlay_l": "0",
                "dipole_lut": "1",
                "overlay_lut": "0",
                "dipole_l": "600",
                "overlay_h": "400"
            },
            "dipole_diameter": 2,
            "templates": [{
                "path": "path/to/atlas/templates",
                "name": "templates name"
            }],
            "dipoles": [
                "IED_axial",
                "IED_sag",
                "IED_coronal",
                "SEF",
                "LEF"
            ],
            "atlas_priority":[
                "atlas71",
                "ICBM_label",
                "atlas116",
                "aal_MNI_V4",
                "TD_lobe"
            ]
        }
      }
    }

Environment Variables

  • MEGHUB_MOME defines the location of the root dir
  • FSLDIR defines the location where FSL is installed
  • DCM2NIIX defines where the dcm2nii is located. this is used to convert dicoms to nifti
  • CAT12STAND defines where the CAT12 script is
  • CAT12DEF defines where the CAT12 deform script is

Normalization Packages

  • FSL FLIRT
  • FSL FNIRT
  • CAT12