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isyangshu / MambaMIL

[MICCAI 2024] Official Code for "MambaMIL: Enhancing Long Sequence Modeling with Sequence Reordering in Computational Pathology"
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Downloading TCGA data #10

Closed MarioPaps closed 2 months ago

MarioPaps commented 6 months ago

I have a question on downloading TCGA data. I used the gdc command line tool to download the WSIs for BRCA. However, a significant number of svs files did not download correctly, resulting in a lot of files with a 'svs.partial' file extension.

Is there a way to avoid this issue so that I can use the max number of WSIs?

wyhsleep commented 6 months ago

You might want to check your network connection.

MarioPaps commented 6 months ago

I was able to download BLCA without issues though. Did you donwload them with gdc client from the terminal or did you use another method?

isyangshu commented 6 months ago

We use the gdc client from the terminal.

MarioPaps commented 6 months ago

Did you download all the files at once? I tried both at once and in stages and some files persist not to download. For example: image