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Merge pull request #666 from dzenanz/removeGDriveLink
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Remove link to our private Google Drive subset of PredictHD dataset
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dzenanz authored Jul 10, 2024
2 parents 07c4891 + 2dd8017 commit 46421f8
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3 changes: 2 additions & 1 deletion miqa/learning/README.md
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Expand Up @@ -13,13 +13,14 @@ pip install -r ./miqa/learning/requirements.txt
```

## Get the data
For example, copy [PredictHD_small](https://drive.google.com/drive/u/1/folders/1SYY5LdKvU6fHgty1ynYXsVzqhGamsZmM) from the shared Google Drive into `nn_work_dir`, as well as files `T1_fold0.csv`, `T1_fold1.csv` and `T1_fold2.csv` from [Learning](https://drive.google.com/drive/u/1/folders/1uT24WMjZLt7IJWPXR-K7YYwiFUSomr_L).
For example, copy `PredictHD_small` from the shared Google Drive into `nn_work_dir`, as well as files `T1_fold0.csv`, `T1_fold1.csv` and `T1_fold2.csv` from `Learning`.
Now edit the paths inside `T1_fold*.csv` files to match the path on your file system, e.g.:
```shell
sed -i 's+P:/PREDICTHD_BIDS_DEFACE/+/home/exampleUser/nn_work_dir/PredictHD_small/+g' T1_fold0.csv
sed -i 's+P:/PREDICTHD_BIDS_DEFACE/+/home/exampleUser/nn_work_dir/PredictHD_small/+g' T1_fold1.csv
sed -i 's+P:/PREDICTHD_BIDS_DEFACE/+/home/exampleUser/nn_work_dir/PredictHD_small/+g' T1_fold2.csv
```
Note: To access [PredictHD](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000222.v6.p2) data, a request needs to be made.

## Run training
To run training on the 3-fold cross-validation using fold 0 as validation set and folds 1 and 2 as training set, use:
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