Fuzzy segmentation issue

[thatsvenyouknow1]

Hey,

I have played around with the Vista3D model as I want to pseudolabel a few CT images from the LIDC dataset for MAISI. Unfortunately, I am encountering a problem where the segmentations look quite fuzzy.

For reproduction:
I am running inference as explained in the README via
export CUDA_VISIBLE_DEVICES=0; python -m scripts.infer --config_file 'configs/infer.yaml' - infer_everything --image_file '<filename>nii.gz'

And this is the minimal code I use to get the LIDC sample:

import pylidc as pl
import nibabel as nib
import numpy as np

os.environ['PYLIDC_PATH'] = '/path/to/LIDC-IDRI' 
patient_id = 'LIDC-IDRI-0001'

#Query for the scan
scan = pl.query(pl.Scan).filter(pl.Scan.patient_id == patient_id).first()

if not scan:
    print(f"Scan with patient ID {patient_id} not found.")
    exit()

#Load scan volume
volume = scan.to_volume() #Gives volume in Hounsfield units
print(f"Volume shape: {volume.shape}") #(512, 512, 133)

#Clip volume (align with a_max and a_min in infer.yaml)
a_max=1053.678477684517
a_min=-963.8247715525971
volume = np.clip(volume, a_min=a_min, a_max=a_max)

#Get voxel spacing
voxel_dims = scan.spacings

#Create affine transformation matrix
affine = np.diag(np.append(voxel_dims, 1))

#Create and save the NIfTI image
nifti_img = nib.Nifti1Image(volume, affine)
output_filename = f"/tmp/{patient_id}.nii.gz"
nib.save(nifti_img, output_filename)
print(f"NIfTI file saved to {output_filename}")

I have also tried varying the transforms and patch size in the infer.yaml without being able to improve the result by much. I would appreciate if you have any hint as to what might be the problem (e.g. data input format, config settings, ...).

Thanks in advance!

[heyufan1995]

Hi @thatsvenyouknow1
Thanks for testing vista3d out! appreciate the feedback. I believe the issue might due to how you save the LIDC data to nifiti file. You should not perform that intensity clip because that's not how MONAI scaleintensity transform (clip =True) work. I'm not familiar with pylidc so not sure if the header part is correct or not.
I downloaded the 'LIDC-IDRI-0001' from https://www.cancerimagingarchive.net/collection/lidc-idri/ and used the following command to convert it to nifti files, you change that path to your downloaded dicom:

dcm2niix -z y -o folder_to_dcm_files .

Then I use monai bundle which wraps this vista3d repo and is much more memory efficient.

pip install monai==1.4.0;
python -m monai.bundle download "vista3d" --bundle_dir "bundles/";
cd bundles/vista3d

and change the input_dict in configs/inference.json to "input_dict": "${'image': 'lidc.nii.gz'}". I ran this command on a 12G old GPU and get the results.

python -m monai.bundle run --config_file configs/inference.json

[thatsvenyouknow1]

Hi @heyufan1995,
Thanks a lot for the quick reply. I applied the "pre-clipping" because the documentation for the ScaleIntensityRange transform specified:

• a_min: intensity original range min (which is -963.82... in the inference json)
• a_max: intensity original range max (which is 1053.67...)

With pre-clipping, the the pylidc data is normalized to values between 0 and 1, whereas without clipping, the data is between -0.54 and 1.99. I thought the goal was probably to have something in the range of [0:1]?

However, thanks to your example, I have figured out that the actual problem was the affine which appears to be used in the Orientation transform.

Thanks again!