JoostJM
commented
3 years ago The issue is indeed in how your paths are formatted in your CSV file. The --validate options shows this; it cannot find the file.
Can you post a line from your csv file (opened using a text editor) including the headers? Maybe I can give you some pointers on how it is formatted.
Are you using relative paths? These should be relative to the folder holding your csv file. As also suggested in #650, are you using backslash escapes for spaces? These should be removed, as all values in the csv are treated as if enclosed in quotes on the cmd line.
HowardEMorgan
ibowennn
Hi,
I am currently attempting to extract features from NIFTI files (.nii.gz) using pyradiomics; however, I am having an issue with the batch feature extraction in the command line using CSV files. I saw that a similar issue was reported in Issue #650. I attempted the suggestions under that thread but am still encountering this issue. I was hoping to ask you if you may have suggestions of what the issue may be that I could evaluate further.
When I attempt to extract features in batch mode from my CSV file, I get the following error stating that there is an "error reading image Filepath or SimpleITK object." [2021-05-07 12:29:54] E: radiomics.script: Feature extraction failed! Traceback (most recent call last): File "C:\Python\Anaconda\lib\site-packages\pyradiomics-3.0.1-py3.8-win-amd64.egg\radiomics\scripts\segment.py", line 70, in _extractFeatures feature_vector.update(extractor.execute(imageFilepath, maskFilepath, label, label_channel)) File "C:\Python\Anaconda\lib\site-packages\pyradiomics-3.0.1-py3.8-win-amd64.egg\radiomics\featureextractor.py", line 272, in execute image, mask = self.loadImage(imageFilepath, maskFilepath, generalInfo, **_settings) File "C:\Python\Anaconda\lib\site-packages\pyradiomics-3.0.1-py3.8-win-amd64.egg\radiomics\featureextractor.py", line 375, in loadImage raise ValueError('Error reading image Filepath or SimpleITK object') ValueError: Error reading image Filepath or SimpleITK object
As also reported in Issue #650, when I use the same paths (copied and pasted directly from my CSV file) in the single extraction mode using "pyradiomics path/to/image path/to/mask --param path/to/YAML -o path/to/Output -f csv" in the command line, this works, and I am able to generate an output file. However, if I do the same with the CSV file, I get the above error.
Per the prior thread, the issue appeared to have resolved when they uninstalled and reinstalled pyradiomics. I attempted this, but the issue is still persisting.
I attempted using prior CSV files that I used to extract features in batch mode about 6 months ago (which were able to be extracted successfully at that time), but I encountered the above error.
I also attempted using --validate as suggested in the prior thread. It reported the following for all cases (last ones shown): [2021-05-07 13:25:14] E: radiomics.script: Image path for case (174/174) does not exist! [2021-05-07 13:25:14] E: radiomics.script: Mask path for case (174/174) does not exist!
Given the features are extracting successfully when extracting single images/masks from the command line individually (using the same paths as those found in the CSV file), I am interpreting this as some sort of issue with reading the paths from the CSV file. I wanted to check if you may have any other suggestions on other things I should try to resolve this?
Happy to hear any suggestions/thoughts about this. Thank you! Howard