some question in the second case which is about pancreas

[hejinchan]

Hi,

When I implement the second case,I have a problem：

Why we should flip label image around y axis ? Because I find that the label of pancreas correspond to the abdominal cavity image,but when flip label image around y axis,they are not corresponding.

and: When I not flip the label image,the result is as the following figure(use 3dslicer to observe the result): the seg1_res.nii.gz and nonlinear_1_3_deformed_seg.nii.gz overlap.

When I flip the label image,the result is as the following figure: we can find that there have a displacement between the seg1_res.nii.gz and nonlinear_1_3_deformed_seg.nii.gz,the displacement make the two images cannot overlap.

Looking forward to your answer！

Thanks!

[chr-wei]

I had a similiar issue with converting the data and moved "-flip y" to the beginning of the c3d call (see pull request #8).

In addition the dcm2niix tool did not work for me somehow and I used this little snippet here to convert dicom files to nifti:

from pathlib import Path
import csv

DATA_ROOT = Path("./nbia_downloaded_data/manifest-1599750808610")

metadata = csv.DictReader(open(DATA_ROOT.joinpath('metadata.csv'), mode='r'))
for entry in metadata:
    # Examine metadata from NBIA data retriever
    subject = entry['Subject ID']
    subject_path = Path(entry['File Location'])
    path = DATA_ROOT.joinpath(subject_path)
    # Retrieve the series id from the dicom directory
    series_dict = !c3d -dicom-series-list {path}
    series_dict = csv.DictReader(series_dict, delimiter='\t')
    series_id = next(series_dict)['SeriesID']

    nii_output_path = INTERMEDIATE_PATH.joinpath(subject + '.nii.gz')
    print(f"Creating '{nii_output_path}' from '{path}'")
    # Read the series from folder selected by id
    !c3d -dicom-series-read {path} {series_id} -o {nii_output_path}