miracle-center / ctspine1k Goto Github PK

hello!!
hope you will be fine i have a issue when i run the Task056_VerSe2019.py the .pkl is created after that it raise error .....

Traceback (most recent call last):
File "Task056_VerSe2019.py", line 127, in
shutil.copy(image_file, join(imagestr, p + "_0000.nii.gz"))
File "/home/projectz-pc2/anaconda3/envs/yolov5_env/lib/python3.8/shutil.py", line 418, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/home/projectz-pc2/anaconda3/envs/yolov5_env/lib/python3.8/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/media/projectz-pc2/Development/Mateen/CTSpine1K-main/nnUNet/dataset_corrOrient/train/1.3.6.1.4.1.9328.50.4.0001.nii.gz'
plz help me to fix it
thank you

Thanks for your contributions!
I download your datasets and want to do segmentations for cervical spine segmentation. But it seems that the floder "HNSCC-3DCT-RT_neck" is the only data I can use, giving other floders doesn't contain areas of cervical spine. But "HNSCC-3DCT-RT_neck" only contain 31 cases. How can I do cervical spine segmentation in this condition like your paper shows?

I am trying to import some NIFTI files from the total segmentator dataset in Slicer 5.2.2. But some files are not open and give an error like this:“[VTK] ReadData: This is not a nrrd file
[VTK] vtkMRMLStorageNode::ReadData: Failed to read node ct (vtkMRMLVectorVolumeNode1) from filename=‘C:/Totalsegmentator_dataset/s0000/ct.nii.gz’
[VTK] vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Failed to instantiate a file reader
[VTK] vtkMRMLStorageNode::ReadData: Failed to read node ct (vtkMRMLVectorVolumeNode2) from filename=‘C:/Totalsegmentator_dataset/s0000/ct.nii.gz’
[VTK] vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read file as a volume of type Volume [fullName = C:/Totalsegmentator_dataset/s0000/ct.nii.gz]: FileFormatError. Number of files listed in the node = 0. File reader says it was able to read 1 files. File reader used the archetype file name of C:/Totalsegmentator_dataset/s0000/ct.nii.gz [reader 0th file name = C:/Totalsegmentator_dataset/s0000/ct.nii.gz].
[VTK] vtkMRMLStorageNode::ReadData: Failed to read node ct (vtkMRMLScalarVolumeNode1) from filename=‘Totalsegmentator_dataset/s0000/ct.nii.gz’
[Qt] void __cdecl qSlicerIOManager::showLoadNodesResultDialog(bool,class vtkMRMLMessageCollection *) Errors occurred while loading nodes: “Error: Loading C:/Totalsegmentator_dataset/s0000/ct.nii.gz - load failed.\n”” I tried the volume, segmentation, and transform options, but they’re not helping. There are 1205 files in the total segmentator dataset, but I cannot open 131 of them. Thanks in advice

Thanks greatly for your contributions with this dataset.
I found a suspicious mask in
colon/1.3.6.1.4.1.9328.50.4.0482.nii.gz
Thought it would be label 15 rather than 14 on the top slices.

Same mistake also:
colon/1.3.6.1.4.1.9328.50.4.0500.nii.gz

Hi,SungDen

Thank you for providing such an amazing dataset,I found there are some errors about the label.
1.Spacing error.

2.label not continue.
(1)1.3.6.1.4.1.9328.50.4.0103_seg.nii.gz

(2)1.3.6.1.4.1.9328.50.4.0291.nii.gz loss label22.

(3)1.3.6.1.4.1.9328.50.4.0730.nii.gz loss label22.

Please can you provide sample inference code for your trained model with minimum hardware requirements and approximate processing time to segment full spine from CT study

(Have tried to email author but no response.)

I use the software MRIcron to view nii.gz files in folder "HNSCC-3DCT-RT_neck". And it looks like this.

How to make the cervical region look more obvious？Like the images in your paper,

Is this dataset only available on Baiduyun? It is very hard to make an account unless you have a Chinese phone number.

Hi,

Thank you for providing such an amazing dataset ;)

I would like to know how to compare with the provided nnUNet baseline. What's the exact dataset split? Could u provide the the data split-id correspondence so that we could compare our own method with your baseline model weights?

Cheers,
Jiancheng Yang