Comments (3)
UPDATE (Jun. 12, 2023) For the publication, our team generated the file 'mimic-cxr-2.0.0-jpeg-txt.csv' by compiling an early-release version of participant notes and text from the images in CXR corresponding to MIMIC-IV. We wanted to add these to this repository, but the data policy from PhysioNet.org states we cannot directly share this compiled data via Git Hub. Physionet is the only one with permission to do so or subsets of the data. This means users need to generate their own mimic-cxr-2.0.0-jpeg-txt.csv based on the released notes and CXR files from Physionet.org once all notes are released. The dataset structure can be inferred from the code. As of June 12, 2023, Physionet has not fully released these notes, but it is likely they are planning to do so as part of their full release of MIMIC-IV. We are very sorry for any inconvenience this may cause.
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Thanks for your response.
Then one question. If I comment the following lines, does it cause any problem in generating the multimodal data?
# # Add paths and info to images in cxr
df_mimic_cxr_jpg =pd.read_csv(core_mimiciv_path + 'mimic-cxr-jpg/2.0.0/mimic-cxr-2.0.0-jpeg-txt.csv')
df_cxr = pd.merge(df_mimic_cxr_jpg, df_cxr, on='dicom_id')
# Save
df_cxr.to_csv(core_mimiciv_path + 'mimic-cxr-jpg/2.0.0/mimic-cxr-2.0.0-metadata.csv', index=False)
#Read back the dataframe
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It should not cause problems, but the input data would not be the same as in the publication. If you don't use the notes of the images, then you may need to comment downstream lines during embedding generation so that the training algorithm is not expecting input text from there. Additionally, you can just make a mimic-cxr-2.0.0-jpeg-txt.csv all with the same text (empty notes).
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Related Issues (16)
- Value of `fname` in `2_3-Pathology Diagnosis Modeling.py` (and also other files) HOT 1
- Request for extracted dataset
- Missing file HOT 3
- Input window for time-series data HOT 4
- Number of training samples HOT 7
- How to use when missing files HOT 9
- Experiments results HOT 1
- Issues loading biobert HOT 2
- Can't locate file HOT 2
- Definitions of records HOT 2
- Patient vs Admission level aggregation
- get_chartevent_tsfresh_timeseries_embeddings has not been called
- Could not find "AUPRC_All_Modality_Resources. csv" HOT 1
- Broken embeddings file on PhysioNet?
- Tensorflow can removed from the requirements
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