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lrsoenksen / HAIM

This repository contains the code to replicate the data processing, modeling and reporting of our Holistic AI in Medicine (HAIM) Publication in Nature Machine Intelligence (Soenksen LR, Ma Y, Zeng C et al. 2022).
Apache License 2.0
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Missing file #3

Closed malika996 closed 1 year ago

malika996 commented 1 year ago

To generate HAIM-MIMIC-MM data using 1_Generate HAIM-MIMIC-MM from downloaded MIMIC-IV and MIMIC-CXR.ipynb, it seems that mimic-cxr-2.0.0-jpeg-txt.csv you're loading, df_mimic-cxr_jpg =pd.read_csv(core_mimiciv_path + 'mimic-cxr-jpg/2.0.0/mimic-cxr-2.0.0-jpeg-txt.csv'), to get image paths plus some extras, is actually missing in MIMIC-CXR-JPG v.2.0.0 database available at physionet.org

struct_mimic-cxr-jpg

How can I access this file?

xunmzii commented 1 year ago

Hi~I have the same trouble in finding 'mimic-cxr-2.0.0-jpeg-txt.csv'. The link you gave on Feb 5 is not accessible now. How can I get access to the file now?

lrsoenksen commented 1 year ago

Hi All data related to MIMIC now needs to be obtained directly through Physionet. Official communication from Physionets states only they can provide credentialed access to any MIMIC data, so posting any of these files in Github is not allowed. Seems that the Physionet group has not yet officially released the notes, so it may be still a few months until you can access them via their website.

xunmzii commented 1 year ago

Okay, thanks for your timely response. Have a beautiful day~