NITRC Automatic Extra-Axial Cerebrospinal Fluid (Auto EACSF) Forum: help

RE: Error: ipGetArgument: argument value of option "-majorityVoting" is missing!

Juan Prieto — Mon, 09 May 2022 22:07:06 GMT

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.

RE: Error: ipGetArgument: argument value of option "-majorityVoting" is missing!

Ayan Mandal — Mon, 09 May 2022 21:35:23 GMT

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"
}
}

RE: Error: ipGetArgument: argument value of option "-majorityVoting" is missing!

Juan Prieto — Mon, 09 May 2022 21:22:43 GMT

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.

Error: ipGetArgument: argument value of option "-majorityVoting" is missing!

Ayan Mandal — Mon, 09 May 2022 20:45:51 GMT

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

RE: Registration

Chieh-En Tseng — Mon, 01 Feb 2021 19:28:18 GMT

Dear Dr. Styner,

I see, thank you very much for your reply and helpful suggestions! I forgot to mention that my data is adult images so the age between the template and data are matching. I will give it a try and see what works best for my data.

Best wishes,
Jane

RE: Registration

Martin Styner — Mon, 01 Feb 2021 19:18:13 GMT

It is not that uncommon for the automatic alignment to fail, particular when a larger portion of the phase and neck is visible. One possibility is to reduce the image content by masking out face & neck regions prior to running the automatic alignment.

You would also have more issues with alignment if the age settings between template and the data is off, e.g. adult template used with infant MRI data. The differences in size will make automatic 6DOF alignment difficult. So make sure to use the age appropriate ICBM template.

Finally, an alternative is to do the ACPC alignment manually. Several existing tools will allow you to do that. I usually use 3DSlicer load both the template and the dataset and then manually adjust the alignment transform (using the Transform module in 3D Slicer). Btw, the General Registration module in 3D Slicer is the same tool (BRAINSFit) used by AutoEACSF to do the alignment, so you could also use a good manual transform as an initialization for the General Registration module

Martin

Registration

Chieh-En Tseng — Mon, 01 Feb 2021 14:57:03 GMT

Hello,

I would like to use the rigid registration provided in the toolbox to ensure that my T1 image is in the correct space and the ACPC line is cut correctly. I used the t1 template from AdultAtlas_ICBM_152_2009a_sym as the template. However, for one of my subjects, the output of the rigid registration does not look good, it is tilted in the coronal view (left side of attached). I then tried to register using FSL's FLIRT outside of the toolbox, using linear registration with 6 DOF, but in this case, the coronal view looks ok and the sagittal view looks a little too tilted and does not look parallel to the ACPC line (right side of attached). I was wondering if there is any recommendation on what to do when the rigid registration from the toolbox is not ideal and how to assess if the registration is good when performing the rigid registration outside the toolbox? Thank you!

RE: Tissue Segmentation Input/Tissue Segmentation Atlas directory

Chieh-En Tseng — Tue, 29 Dec 2020 19:01:42 GMT

Hi Juan,

Thank you, it worked after using a binary mask!

Hope you have a Happy New Year!

Best wishes,
Jane

RE: Tissue Segmentation Input/Tissue Segmentation Atlas directory

Juan Prieto — Tue, 29 Dec 2020 17:00:16 GMT

[color=#000000]Hi, [/color]

I think I found the issue.
Since you are providing a brainmask, it should be a [b]binary[/b] mask.

If you check the output 'brainmask_orientOK_ACPC_Erosion00.nrrd' it has multiple labels but this output should have the eroded brainmask only.
The following steps will likely fail because of this.

Please let me know how it goes.

Best,

[i]Originally posted by Chieh-En Tseng:[/i][quote]Hi Juan,

Thank you for your quick reply. I am not using the rigid registration option because it is disabled after I input my brainmask in Step 1 and I did not check the automatic skullstripping option. My brainmask is registered to my T1 image and the skullstripped image looks good.

The _labels_EMS.nrrd file looks good too, I see that it has segmented my image. I think even the MID0 files in the FinalMasking folder look ok, but not sure why I don't see anything in the QCistern file.

I am copying a link here with more files https://drive.google.com/file/d/1CRu7RxDKqieAJlVyk6Onz1L6G6TW6fe5/view?usp=sharing.

Thank you again!

Best wishes,
Jane[/quote]

RE: Tissue Segmentation Input/Tissue Segmentation Atlas directory

Chieh-En Tseng — Tue, 29 Dec 2020 16:41:42 GMT

Hi Juan,

Thank you for your quick reply. I am not using the rigid registration option because it is disabled after I input my brainmask in Step 1 and I did not check the automatic skullstripping option. My brainmask is registered to my T1 image and the skullstripped image looks good.

The _labels_EMS.nrrd file looks good too, I see that it has segmented my image. I think even the MID0 files in the FinalMasking folder look ok, but not sure why I don't see anything in the QCistern file.

I am copying a link here with more files https://drive.google.com/file/d/1CRu7RxDKqieAJlVyk6Onz1L6G6TW6fe5/view?usp=sharing.

Thank you again!

Best wishes,
Jane