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Please help cann't read data #28
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My python version is 3.7. pipenv package: |
i will appreciate your help in this matter! |
@Amir-Reza-Sadri take a look |
Thank you for reaching out. Based on the tool's message: "The input folder is empty or includes unsupported file formats!", please ensure the following:
If you're still facing issues, please share a sample of your input data or the list of file types you're trying to process. I'd be happy to take a closer look and assist you further. |
Any ideas about this? |
Thank you for reaching out and providing the details of the error you encountered. Based on the error message "ValueError: Third dimension must be 3 or 4", it appears that the issue is related to the dimensionality of the image data being processed. Our tool is designed to work with medical imaging standard formats, which typically do not include color channels as seen in standard RGB or RGBA images. It seems the data you are attempting to process may contain color information, which is not supported by our tool. To resolve this, please ensure that the images are in a supported medical imaging format (like DICOM, NIfTI, or similar grayscale formats) before passing them to the tool. If you are working with non-medical standard color images, you might need to convert them to grayscale or extract the relevant channels to fit the expected input format for the tool. If you're indeed working with medical images and still encountering this error, please double-check that the images have not been inadvertently converted to a color format during preprocessing or loading. The tool expects the input data to be in grayscale with a shape that corresponds to (height, width) for 2D images or (slices, height, width) for 3D volumes. Let me know if you need further assistance or if there are any additional details you can provide. |
These are standard nii images from a Siemens 3T Prisma. No color, standard dicom to nifti conversion. They are BOLD images 4D (slices, height, width, time). Can MRQy could handle 4D? |
see #17 |
I used pipenv to run the MRQY。
input:(a4020-WYmTOfA1) (base) C:\Users\a4020\Documents\GitHub\MRQy\src\mrqy>python QC.py MR_RAW 'C:\Users\a4020\Desktop\mrqy learning\MR-nii'
output:MRQy is starting....
The number of patients is 0
The input folder is empty or includes unsupported files format!
Skipped the t-SNE and UMAP computation because of insufficient data. The UMAP and t-SNE process need at least 6 input data.
Traceback (most recent call last):
File "QC.py", line 376, in
df = tsv_to_dataframe(address)
File "QC.py", line 205, in tsv_to_dataframe
return pd.read_csv(tsvfileaddress, sep='\t', skiprows=2, header=0)
File "C:\Users\a4020.virtualenvs\a4020-WYmTOfA1\lib\site-packages\pandas\io\parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "C:\Users\a4020.virtualenvs\a4020-WYmTOfA1\lib\site-packages\pandas\io\parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "C:\Users\a4020.virtualenvs\a4020-WYmTOfA1\lib\site-packages\pandas\io\parsers.py", line 948, in init
self._make_engine(self.engine)
File "C:\Users\a4020.virtualenvs\a4020-WYmTOfA1\lib\site-packages\pandas\io\parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "C:\Users\a4020.virtualenvs\a4020-WYmTOfA1\lib\site-packages\pandas\io\parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas_libs\parsers.pyx", line 540, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
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