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