Hello,

I'm running auto_EACSF through the GUI on an HPC with ITK 4.13 with just a T1, not T2. I'm running into the error message indicated in the title, that an argument value for "-majorityVoting" is missing, resulting in the "[T1]_stx_weightedMajority.nii.gz" not being created. The problematic line of code (produced from the make_mask.py script) appears to be the following:

/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/ImageMath /gpfs/fs001/cbica/projects/bgdimagecentral/Data/hao_data/Hao-inf-011/mri/output/SkullStripping/Hao-inf-011_T1w_stx.nii.gz -majorityVoting -outfile /gpfs/fs001/cbica/projects/bgdimagecentral/Data/hao_data/Hao-inf-011/mri/output/SkullStripping/Hao-inf-011_T1w_stx_weightedMajority.nii.gz

Any tips on how I could debug this error? A copy of the full error log is attached:

Thanks,
Ayan

Can you share your input configuration? It is the .json file created in your output directory. 

To debug, you can also run the application directly using python on your terminal.
You can run the main_script.py and it will give you more information about the execution.

Here it is! I've tried running main_script.py from the command line too but it hasn't given me much more info unfortunately. Thank you for your help!

{
"data": {
"BrainMask": "",
"CerebellumMask": "",
"SubjectVentricleMask": "",
"T1img": "/gpfs/fs001/cbica/projects/bgdimagecentral/Data/hao_data/Hao-inf-011/mri/Hao-inf-011_T1w.nii.gz",
"T2img": "",
"TissueSeg": "",
"output_dir": "/gpfs/fs001/cbica/projects/bgdimagecentral/Data/hao_data/Hao-inf-011/mri/output"
},
"executables": [
{
"name": "ABC_CLI",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/ABC_CLI"
},
{
"name": "ANTS",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/ANTS"
},
{
"name": "BRAINSFit",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/BRAINSFit"
},
{
"name": "ImageMath",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/ImageMath"
},
{
"name": "ImageStat",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/ImageStat"
},
{
"name": "WarpImageMultiTransform",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/WarpImageMultiTransform"
},
{
"name": "bet",
"path": "/cbica/software/external/fsl/centos7/5.0.11/bin/bet"
},
{
"name": "convertITKformats",
"path": "/gpfs/fs001/cbica/software/external/auto_EACSF/1.7.7/bin/convertITKformats"
},
{
"name": "python3",
"path": "/cbica/external/python/anaconda/3/envs/auto_EACSF/bin/python3"
}
],
"parameters": {
"ACPC_UNIT": "index",
"ACPC_VAL": 70,
"ANTS_T1_weight": 1,
"ANTS_gaussian_sig": 3,
"ANTS_iterations_val": "100x50x25",
"ANTS_reg_type": "GreedyDiffeo",
"ANTS_sim_metric": "CC",
"ANTS_sim_param": 4,
"ANTS_transformation_step": 0.25,
"COMPUTE_CSFDENS": false,
"CSFLabel": 3,
"LH_innerSurface": "",
"PERFORM_REG": true,
"PERFORM_SS": true,
"PERFORM_TSEG": true,
"PERFORM_VR": true,
"RH_innerSurface": "",
"USE_DCM": true,
"atlas_obj": {
},
"registrationAtlas": "/cbica/projects/bgdimagecentral/templates/pediatric-atlas-1year-T1-ABC/1year-Average-IBIS-MNI-t1w.nrrd",
"skullStrippingAtlasesDirectory": "",
"templateInvMaskVentricle": "/cbica/projects/bgdimagecentral/templates/pediatric-atlas-1year-T1-ABC/DeepGray5Class_stripped/Vent_CSF-INVMask.nrrd",
"templateT1Ventricle": "/cbica/projects/bgdimagecentral/templates/pediatric-atlas-1year-T1-ABC/DeepGray5Class_stripped/T1-IGM.nrrd",
"tissueSegAtlasDirectory": "/cbica/projects/bgdimagecentral/templates/pediatric-atlas-1year-T1-ABC/DeepGray5Class_stripped"
}
}

You are missing some configuration for the Skull Stripping step. 

Please download the zip file brainmaskingMultiatlas_part1.zip at https://www.nitrc.org/frs/?group_id=1322

You should provide the directory as input for the skull stripping step.